Methods of predicting clinical course and treating multiple sclerosis

ABSTRACT

Provided are methods and kits for classifying a subject as being more likely to have benign multiple sclerosis (BMS) or as being more likely to have typical relapsing remitting multiple sclerosis (RRMS). Classification of multiple sclerosis disease course is performed by comparing a level of expression of at least one gene involved in the RNA polymerase I pathway in a cell of the subject to a reference expression data of said at least one gene obtained from a cell of at least one subject pre-diagnosed as having BMS and/or from a cell of at least one subject pre-diagnosed as having typical RRMS, thereby classifying the subject as being more likely to have BMS or as being more likely to have typical RRMS. Also provided are methods of diagnosing and treating multiple sclerosis and methods of monitoring treatment efficiency.

RELATED APPLICATIONS

This application is a division of U.S. patent application Ser. No.13/260,573 filed on Sep. 27, 2011, which is a National Phase of PCTPatent Application No. PCT/IB2010/051344 having International filingdate of Mar. 28, 2010, which claims the benefit of priority of U.S.Provisional Patent Application No. 61/202,703 filed on Mar. 30, 2009.The contents of the above applications are all incorporated herein byreference.

SEQUENCE LISTING STATEMENT

The ASCII file, entitled 62191SequenceListing.txt, created on Sep. 27,2011, comprising 7,168,844 bytes, submitted concurrently with the filingof this application is incorporated herein by reference.

FIELD AND BACKGROUND OF THE INVENTION

The present invention, in some embodiments thereof, relates to methodsof classifying a subject as having benign multiple sclerosis or typicalrelapsing remitting multiple sclerosis and, more particularly, but notexclusively, to methods of treating multiple sclerosis based on same.

Multiple sclerosis (MS) is the most common demyelinating disease of thecentral nervous system (CNS) affecting young adults (disease onsetbetween 20 to 40 years of age) and is the third leading cause fordisability after trauma and rheumatic diseases, with an estimated annualcost 34,000 USD per patient (total life time cost of 2.2 million USD perpatient).

The disease is characterized by destruction of myelin, associated withdeath of oligodendrocytes and axonal loss. The main pathologic findingin MS is the presence of infiltrating mononuclear cells, predominantly Tlymphocytes and macrophages, which surpass the blood brain barrier andinduce an active inflammation within the brain and spinal cord. Theneurological symptoms that characterize MS include complete or partialvision loss, diplopia, sensory symptoms, motor weakness that can worsento complete paralysis, bladder dysfunction and cognitive deficits, whicheventually may lead to a significant disability. The associated multipleinflammatory foci lead to myelin destruction, plaques of demyelination,gliosis and axonal loss within the brain and spinal cord and are thereasons contribute to the clinical manifestations of neurologicaldisability.

The etiology of MS is not fully understood. The disease develops ingenetically predisposed subjects exposed to yet undefined environmentalfactors and the pathogenesis involves autoimmune mechanisms associatedwith autoreactive T cells against myelin antigens. It is wellestablished that not one dominant gene determines genetic susceptibilityto develop MS, but rather many genes, each with different influence, areinvolved.

Clinically, in 85% of MS patients the illness is initiated with arelapsing-remitting course (RRMS), and in about 10-15% of MS patientshave an a-priori primary progressive course (PPMS) without relapses.RRMS is characterized by inflammatory attacks associated withneurological deficits with periods of remissions between the relapsesthat vary in time. After a period of 10 years, about 50% of RRMSpatients will progress to a secondary progressive MS (SPMS) course,characterized by permanent neurological dysfunction, with or withoutrelapses and progressive disability.

Benign M S (BMS) is a clinical variant of RRMS in which the patientsdevelop low neurological disability if at all after a disease durationof at least 10 years. Accordingly, this group of MS patients do notexperience devastating accumulating disability over-time and when thesepatients are examined neurologically and scored by the ExpandedDisability Status Scale (EDSS) they receive a score that is equal to orlower than 3.0. This low EDSS score signifies mild disability and whenthis low disability occurs more than 10 years after disease onset, thecourse of MS is defined as benign (Pittock S J and Rodriguez M, 2008;Costelloe, L., et al., 2008). Prediction of patients that will have BMSis currently impossible and the definition of these patients isretrospective. The molecular events accountable for the BMS variant ofdisease are not understood.

Diterpenoid triepoxide Triptolide (TPT), isolated from the Chinese herbTripterygium wilfordii (Leuenroth S J and Crews C M. Triptolide-inducedtranscriptional arrest is associated with changes in nuclearsubstructure. Cancer Res. 2008; 68:5257-5266) has variousanti-inflammatory effects (Liu Y, et al. Triptolide, a component ofChinese herbal medicine, modulates the functional phenotype of dendriticcells. Transplantation. 2007; 84:1517-1526), it modulates T-cellinflammatory responses and ameliorates Experimental AutoimmuneEncephalomyelitis (Wang Y, et al. Triptolide modulates T-cellinflammatory responses and ameliorates experimental autoimmuneencephalomyelitis. J Neurosci Res. 2008; 86:2441-2449). Derivatives ofTPT were suggested for treating autoimmune diseases (EP 0983256,PCT/US1998/008562; WO9852933A1).

Cycloheximide, inhibits the phosphorylation of RRN3 and causes itsdissociation from RNA polymerase I. RRN3 interacts with the rpa43subunit of RNA polymerase I, and treatment with cycloheximide inhibitsthe formation of a RRN3/rpa43 complex in vivo (Alice H. Cavanaugh, etal., 2002. Rrn3 Phosphorylation is a regulatory checkpoint for ribosomebiogenesis J. Biol. Chem., 2002; 277: 27423-27432).

PCT Application No. PCT/IL2007/32856 discloses methods and kits forpredicting prognosis of multiple sclerosis.

PCT Application No. PCT/IL2007/001617 discloses methods and kits forpredicting the prognosis of a subject diagnosed with multiple sclerosisand methods of selecting a treatment regimen of a subject diagnosed withmultiple sclerosis.

Achiron A, et al., 2007 (Clinical and Experimental Immunology, 149:235-242) describe genes of the zinc-ion binding and cytokine activityregulation pathways which predict outcome in relapsing—remittingmultiple sclerosis.

Additional background art includes PCT Pub. No. WO03081201A2.

SUMMARY OF THE INVENTION

According to an aspect of some embodiments of the present inventionthere is provided a method of classifying a subject as being more likelyto have benign multiple sclerosis (BMS) or as being more likely to havetypical relapsing remitting multiple sclerosis (RRMS), the methodcomprising comparing a level of expression of at least one gene involvedin the RNA polymerase I pathway in a cell of the subject to a referenceexpression data of the at least one gene obtained from a cell of atleast one subject pre-diagnosed as having BMS and/or from a cell of atleast one subject pre-diagnosed as having typical RRMS, therebyclassifying the subject as being more likely to have BMS or as beingmore likely to have typical RRMS.

According to an aspect of some embodiments of the present inventionthere is provided a method of diagnosing a subject pre-diagnosed withmultiple sclerosis (MS) as having benign multiple sclerosis (BMS) ortypical relapsing remitting multiple sclerosis (RRMS), the methodcomprising:

(a) classifying the subject as being more likely to have BMS or as beingmore likely to have typical RRMS according to the method of the presentinvention,

(i) wherein when the subject is classified as being more likely to havethe BMS then the subject is diagnosed as having BMS;

(ii) wherein when the subject is classified as being more likely to havethe typical RRMS, then the subject is diagnosed as having typical RRMS;and

(c) informing the subject of the diagnosis,

thereby diagnosing the subject pre-diagnosed with the MS as having theBMS or the typical RRMS.

According to an aspect of some embodiments of the present inventionthere is provided a method of monitoring an efficiency of an antimultiple sclerosis (MS) drug in treating a subject diagnosed with atypical relapsing remitting multiple sclerosis (RRMS) course, the methodcomprising:

(a) treating the subject with the anti MS drug; and

(b) comparing a level of expression of least one gene involved in theRNA polymerase I pathway in a cell of the subject following the treatingwith the anti MS drug to a level of expression of the at least one genein a cell of the subject prior to the treating the subject with the antiMS drug,

(i) wherein a decrease above a predetermined threshold in the level ofexpression of the at least one gene following the treating with the antiMS drug relative to the level of expression of the at least one geneprior to the treating with the anti MS drug indicates that the anti MSdrug is efficient for treating the subject;

(ii) wherein an increase above a predetermined threshold in the level ofexpression of the at least one gene following the treating with the antiMS drug relative to the level of expression of the at least one geneprior to the treating with the anti MS drug indicates that the anti MSdrug is not efficient for treating the subject; or

(iii) wherein when a level of expression of the at least one genefollowing the treating with the anti MS drug is identical or changedbelow a predetermined threshold as compared to prior to the treatingwith the anti MS drug then the treatment is not efficient for treatingthe subject.

thereby monitoring the efficiency of the anti multiple sclerosis (MS)drug in treating the subject diagnosed with the typical RRMS course.

According to an aspect of some embodiments of the present inventionthere is provided an in vitro method of predicting an efficiency of ananti multiple sclerosis (MS) drug for treatment of a subject diagnosedwith a typical relapsing remitting multiple sclerosis (RRMS), the methodcomprising:

(a) contacting cells of the subject with a therapeutically effectiveamount of the anti MS drug; and

(b) comparing a level of expression in the cells of at least one geneinvolved in the RNA polymerase I pathway following the contacting withthe anti MS drug to a level of expression of the at least one gene inthe cells prior to the contacting with the anti MS drug,

(i) wherein a decrease above a predetermined threshold in the level ofexpression of the at least one gene following the contacting with theanti MS drug relative to the level of expression of the at least onegene prior to the contacting with the anti MS drug indicates that thetreatment is efficient for treating the subject;

(ii) wherein an increase above a predetermined threshold in the level ofexpression of the at least one gene following the contacting with theanti MS drug relative to the level of expression of the at least onegene prior to the contacting with the anti MS drug indicates that thetreatment is not efficient for treating the subject; or

(iii) wherein when a level of expression of the at least one genefollowing the contacting with the anti MS drug is identical or changedbelow a predetermined threshold as compared to prior to the contactingwith the anti MS drug then the treatment is not efficient for treatingthe subject.

thereby predicting the efficiency of the anti MS drug for treatment ofthe subject diagnosed with the typical RRMS.

According to an aspect of some embodiments of the present inventionthere is provided a method of treating a subject diagnosed with multiplesclerosis, the method comprising

(a) classifying the subject as being more likely to have BMS or typicalRRMS according to the method of the present invention,

(b) selecting a treatment regimen based on classification results ofstep (a); thereby treating the subject diagnosed with multiplesclerosis.

According to an aspect of some embodiments of the present inventionthere is provided a method of treating a subject diagnosed with multiplesclerosis, the method comprising:

(a) diagnosing a typical relapsing remitting multiple sclerosis (RRMS)according to the method of the present invention,

(b) administering to the subject a therapeutically effective amount ofditerpenoid triepoxide Triptolide (TPT) or a derivative thereof, therebytreating the subject.

According to an aspect of some embodiments of the present inventionthere is provided a probeset comprising a plurality of oligonucleotidesand no more than 50 oligonucleotides, wherein an oligonucleotide of theplurality of oligonucleotides specifically recognizes a polynucleotideof at least one gene involved in the RNA polymerase pathway.

According to an aspect of some embodiments of the present inventionthere is provided a kit for classifying a disease course in a subjectdiagnosed with multiple sclerosis (MS), comprising the probeset of thepresent invention.

According to an aspect of some embodiments of the present inventionthere is provided a method of selecting a drug for treating a typicalrelapsing remitting multiple sclerosis (RRMS) in a subject, the methodcomprising:

contacting cells of a subject classified as having a typical RRMS with aplurality of drug molecules,

identifying at least one drug molecule which downregulates a level ofexpression of at least one gene involved in the RNA polymerase Ipathway, the at least one drug molecule is suitable for treating thetypical RRMS in the subject,

thereby selecting the drug for treating the typical RRMS in the subject.

According to some embodiments of the invention, a decrease above apredetermined threshold in the level of expression of the at least onegene in the cell of the subject relative to the reference expressiondata of the at least one gene obtained from the at least one subjecthaving the typical RRMS classifies the subject as being more likely tohave the BMS.

According to some embodiments of the invention, an increase above apredetermined threshold in the level of expression of the at least onegene in the cell of the subject relative to the reference expressiondata of the at least one gene obtained from the at least one subjecthaving the BMS classifies the subject as being more likely to have thetypical RRMS.

According to some embodiments of the invention, a level of expression ofthe at least one gene in the cell of the subject is identical or changedbelow a predetermined threshold as compared to the reference expressiondata of the at least one gene obtained from the at least one subjecthaving the BMS, then the subject is classified as being more likely tohave the BMS.

According to some embodiments of the invention, a level of expression ofthe at least one gene in the cell of the subject is identical or changedbelow a predetermined threshold as compared to the reference expressiondata of the at least one gene obtained from the at least one subjecthaving the typical RRMS, then the subject is classified as being morelikely to have the typical RRMS.

According to some embodiments of the invention, when the subject beingmore likely to have typical RRMS then the treatment regimen comprisesadministering to the subject an agent which downregulates the level ofexpression of the at least one gene involved in the RNA polymerase Ipathway.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway is selected from the groupconsisting of POLR1D, LRPPRC, RRN3 and NCL.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway comprises the POLR1D, LRPPRC,RRN3 and NCL genes.

According to some embodiments of the invention, the agent is selectedfrom the group consisting of an siRNA, an antisense, an antibody and asmall molecule.

According to some embodiments of the invention, the small molecule isCycloheximide

According to some embodiments of the invention, the at least one gene isRRN3, and whereas the downregulating is effected using diterpenoidtriepoxide Triptolide (TPT) or a derivative thereof.

According to some embodiments of the invention, the at least one gene isRRN3, and whereas the downregulating is effected using Cycloheximide

According to some embodiments of the invention, the kit furthercomprising a positive control for an expression level of the at leastone gene involved in the RNA polymerase pathway.

According to some embodiments of the invention, each of the plurality ofoligonucleotides is bound to a solid support.

According to some embodiments of the invention, the plurality ofoligonucleotides are bound to the solid support in an addressablelocation.

According to some embodiments of the invention, the level of expressionis determined using an RNA detection method.

According to some embodiments of the invention, the level of expressionis determined using a protein detection method.

According to some embodiments of the invention, the cell is a bloodcell.

According to some embodiments of the invention, the method furthercomprising administering to the subject a therapeutically effectiveamount of an anti MS agent.

According to some embodiments of the invention, the anti-MS agent isselected from the group consisting of Diterpenoid triepoxide Triptolide(TPT), Adderall, Ambien, Avonex, Baclofen, Beta interferon, Betaseron,Celexa, Clonazepam, Copaxone, Corticosteroids, Cymbalta, Cytoxan,Dexamethasone, Effexor, Elavil, Gabapentin, Hydrocodone, Lexapro,Lyrica, Mitoxantrone, Naltrexone, Neurontin, Novantrone, Prednisone,Provigil, Rebif, Solumedrol, Symmetrel, Topamax, Tysabri, Wellbutrin,Xanax, Zanaflex, Zoloft, fingolimod, laquinimod, Mylinax (cladribine),teriflunomide, BG-12 (Biogen Idec's), firategrast (GSK/Mitsubishi TanabePharma), ibudilast (MediciNova's), and CDP323 (Biogen/UCB).

According to an aspect of some embodiments of the present inventionthere is provided a method of predicting a benign multiple sclerosiscourse in a subject diagnosed with multiple sclerosis, the methodcomprising: (a) determining in a biological sample of the subject alevel of expression of at least one polynucleotide selected from thegroup consisting of C22orf8, TLK1, HNRPH1, PLXDC1, TLK1, PKN2, ALS2CR8,FLJ12547, ZNF238, PDPR, NT5E, PASK, HPGD, IL6ST, JARID1A, PASK, LEF1,FLJ10246, MTUS1, FLJ14011, VSIG4, MARCH-VI, FLJ10613, EWSR1, ATP8A1,SLC4A7, FLJ21127, HNRPH1, ABLIM1, ITGA6, ADCY9, CROCC, SH3YL1, SMA4,SPTBN1, DPEP3, PDE3B, AF5Q31, NRCAM, DOCK9, IPW, FLJ20152, SIRPB2,GALNT4, CD28, TXK, ETS1, DGCR5, ZNF192, TCF7, CAMK4, SIM2, MGEA5,TGFBR2, RET, MAPK8IP3, RRN3, DKFZp547H025, FBXW11, ZNF423, DLG1,MGC17330, CD164L1, REPS1, ACHE, ITGB1BP2, LOC94431, LTK, RUNX1, EVER1,KIAA2010, CEACAM7, STX16, SLC4A5, CRTAP, RECQL5, MAGEF1, VIPR1,FLJ10979, TTC3, CRSP2, BAZ2A, GTF2I, MGC50853, KIAA0508, BPHL, LTBP4,FN3KRP, SCARB1, MGC17330, HYAL4, DGKA, FLJ11196, DHRS6, EPHB4,IDI2/GTPBP4, SNTG2, SLC7A6, PMS2L2, KIAA0436, TOSO, THRAP3, T3JAM,LOC283232, LOC92482, PTER, ATM, NUCB2, PIK3R2, MGC1136, CD59, JARID1A,FLJ39616, ABLIM1, PBP, MAPK8IP3, FTS, LHX5, TNFRSF7, MYC, PBXIP1, DATF1,HTF9C, PUS1, KIAA0924, C6orf4, KIAA0372, WDR42A, CRYZL1, TERE1, LTBP4,TTC3, NFATC1, POM121/LOC340318, TOSO, LOC348926/MGC16279/SB153/FLJ10661,SPOCK2, KIAA0515, SLC37A4, CD44, SMARCA2, SPTBN1, C6orf130, TTC3, DLG1,SLC35E2, MCCC1, PMS2L11, RCN3, STX16, FLJ20618, STAT5B, SMARCA2, SATB1,POLR1D, ASXL1, REV1L, PMS2L2/PMS2L5, FLJ12355, CCNB1IP1, FLJ12270,KIAA0692, MCM7, GPSN2, STX16, MMS19L, GTF2I/GTF2IP1, AKAP7, ZNF444,SLC35A3, MGEA5, RUTBC3, C20orf36, RAD17, ALG12, LOC112869, C6orf48,CUTC, LGTN, DEF6, WAC, HNRPH3, NS, KIAA0892, LRPPRC, HMG20A, DDX42,TINP1, ZDHHC17, C19orf2, EIF4B, LOC376745, DKFZP434C171, TH1L, C19orf13,RPL22, PHF15, EWSR1, EIF4B, FAM48A, YT521, NEK9, EIF3S7, RPS6, RPL35A,EEF2, RPL3, RPS6, UBA52, RPL6, RPS6, RPL13, AL353949, AL580863,AF052160, AW128846, AW974481, N92920, BG178274, AW303460, BF057458,AL050035, M59917, AK025422, AI693985, AU158442, AK021460, AL023773,NM_003790, AC005011, M90355, AL353580, U38964, D50683 and BE967207,wherein downregulation below a predetermined threshold in the level ofexpression relative to a level of expression of the at least onepolynucleotide in a biological sample of a subject diagnosed withtypical relapsing-remitting multiple sclerosis (RRMS) is indicative ofthe prediction of the benign multiple sclerosis course of the subject;(b) informing the subject of the prediction of the benign multiplesclerosis course; thereby predicting the benign multiple sclerosiscourse in the subject diagnosed with the multiple sclerosis.

According to an aspect of some embodiments of the present inventionthere is provided a method of predicting a benign multiple sclerosiscourse in a subject diagnosed with multiple sclerosis, the methodcomprising: (a) determining in a biological sample of the subject alevel of expression of at least one polynucleotide selected from thegroup consisting of YWHAB, ATP6V1E1, UBB, MRLC2/MRCL3, UQCR, MRLC2,RTN4, UBE2A, RTN4, WDR1, PSMA6, C14orf123, PP1201, TBK1, CAST, CAST,RSN, PSME1, SDF2, GSTO1, CAST, DNCL1, SQRDL, ADIPOR2, ICMT, NDUFA6,NDUFA6, COX17, HIF1AN, FLJ20257, TBPL1, RAPGEF2, CRSP8, APOL1, PAOX,CNDP2, ETFA, DPP3, KPNA1, MGC3036, TUBB2, PDCL, CCL5, CDS2, RAP1GDS1,ATP6V1D, OBRGRP/LEPR, SF4, GCLC, MGST3, BICD2, BRF1, CHST12, EXOSC7,TOR1B, ZFP95, ILK, UNC13A, MTHFD2, CASP10, FLJ45850, CMRF-35H, ARF3,NDOR1, DUSP10, AP1M2, VRK2, GSN, PTRF, RBM19, RABGAP1L, ATP5S, STOM,TFPI2, SLCO3A1, PTPN12, CSF1, SIGLEC6, KIRREL, OBRGRP, TP53AP1, SUHW1,NUP98, IL15RA, MICB, CMRF-35H, SPHK1, TNFRSF6, FLJ1301, LRP5, STOM,EPHA2, SRC, FLJ11301, PSTPIP2, EBP, MCPH1, PTPRF, LIMK2, FSTL4, CBR1,MGC2654, MYCT1, NOL3, MITF, ATP10B, FBXO31, TBX21, LSS, SLC17A3, MNAB,CHPPR, GIF, VAMPS, ABCG2, KIF1B, LOH11CR2A, NID2, RBBP8, ETV7, CTSL,RUFY1, RSU1, PARD3, APOB, ACOX3, DAB2, LDLR, TJP2, GNAS, PARD3, NCKAP1,TAP2, HDGFRP3, LDLR, PIK3R3, HTR2B, GAS2L1, FER1L3, C3orf14, TP53TG3,LEPR, CLIC5, PDE4DIP, ATP9A, ITGB1BP1, INDO, SELP, FHL2, FER1L3, EGF,SIAT8A, HDGFRP3, LRAP, VWF, FLJ10134, IMP-3, DMN, MCTP1, FSTL1, CTNNAL1,RAB27B, THBS1, PROS1, MMRN1, CTTN, AL078596, AI148659, U00956 andM29383, wherein upregulation above a predetermined threshold in thelevel of expression relative to a level of expression of the at leastone polynucleotide in a biological sample of a subject diagnosed withtypical relapsing-remitting multiple sclerosis (RRMS) is indicative ofthe prediction of the benign multiple sclerosis course of the subject;(b) informing the subject of the prediction of the benign multiplesclerosis course; thereby predicting the benign multiple sclerosiscourse in the subject diagnosed with the multiple sclerosis.

According to an aspect of some embodiments of the present inventionthere is provided a method of monitoring treatment with an anti MS drugin a subject in need thereof, the method comprising: (a) treating thesubject with the anti MS drug; and (b) determining in a biologicalsample of the subject a level of expression of at least onepolynucleotide selected from the group consisting of YWHAB, ATP6V1E1,UBB, MRLC2/MRCL3, UQCR, MRLC2, RTN4, UBE2A, RTN4, WDR1, PSMA6,C14orf123, PP1201, TBK1, CAST, CAST, RSN, PSME1, SDF2, GSTO1, CAST,DNCL1, SQRDL, ADIPOR2, ICMT, NDUFA6, NDUFA6, COX17, HIF1AN, FLJ20257,TBPL1, RAPGEF2, CRSP8, APOL1, PAOX, CNDP2, ETFA, DPP3, KPNA1, MGC3036,TUBB2, PDCL, CCL5, CDS2, RAP1GDS1, ATP6V1D, OBRGRP/LEPR, SF4, GCLC,MGST3, BICD2, BRF1, CHST12, EXOSC7, TOR1B, ZFP95, ILK, UNC13A, MTHFD2,CASP10, FLJ45850, CMRF-35H, ARF3, NDOR1, DUSP10, AP1M2, VRK2, GSN, PTRF,RBM19, RABGAP1L, ATP5S, STOM, TFPI2, SLCO3A1, PTPN12, CSF1, SIGLEC6,KIRREL, OBRGRP, TP53AP1, SUHW1, NUP98, IL15RA, MICB, CMRF-35H, SPHK1,TNFRSF6, FLJ11301, LRP5, STOM, EPHA2, SRC, FLJ11301, PSTPIP2, EBP,MCPH1, PTPRF, LIMK2, FSTL4, CBR1, MGC2654, MYCT1, NOL3, MITF, ATP10B,FBXO31, TBX21, LSS, SLC17A3, MNAB, CHPPR, GIF, VAMPS, ABCG2, KIF1B,LOH11CR2A, NID2, RBBP8, ETV7, CTSL, RUFY1, RSU1, PARD3, APOB, ACOX3,DAB2, LDLR, TJP2, GNAS, PARD3, NCKAP1, TAP2, HDGFRP3, LDLR, PIK3R3,HTR2B, GAS2L1, FER1L3, C3orf14, TP53TG3, LEPR, CLIC5, PDE4DIP, ATP9A,ITGB1BP1, INDO, SELP, FHL2, FER1L3, EGF, SIAT8A, HDGFRP3, LRAP, VWF,FLJ10134, IMP-3, DMN, MCTP1, FSTL1, CTNNAL1, RAB27B, THBS1, PROS1,MMRN1, CTTN, AL078596, AI148659, U00956 and M29383, wherein anupregulation above a predetermined threshold in the level of expressionrelative to a level of expression of the at least one polynucleotide ina biological sample of a subject diagnosed with typicalrelapsing-remitting multiple sclerosis (RRMS) is indicative of treatmentefficacy.

According to some embodiments of the invention, step (b) is effectedalso prior to step (a) and wherein the upregulation is with respect to alevel of the at least one polynucleotide prior to the treating.

According to an aspect of some embodiments of the present inventionthere is provided a method of monitoring treatment with an anti MS drugin a subject in need thereof, the method comprising: (a) treating thesubject with the anti MS drug; and (b) determining in a biologicalsample of the subject a level of expression of at least onepolynucleotide selected from the group consisting of C22orf8, TLK1,HNRPH1, PLXDC1, TLK1, PKN2, ALS2CR8, FLJ12547, ZNF238, PDPR, NT5E, PASK,HPGD, IL6ST, JARID1A, PASK, LEF1, FLJ10246, MTUS1, FLJ14011, VSIG4,MARCH-VI, FLJ10613, EWSR1, ATP8A1, SLC4A7, FLJ21127, HNRPH1, ABLIM1,ITGA6, ADCY9, CROCC, SH3YL1, SMA4, SPTBN1, DPEP3, PDE3B, AF5Q31, NRCAM,DOCK9, IPW, FLJ20152, SIRPB2, GALNT4, CD28, TXK, ETS1, DGCR5, ZNF192,TCF7, CAMK4, SIM2, MGEA5, TGFBR2, RET, MAPK8IP3, RRN3, DKFZp547H025,FBXW11, ZNF423, DLG1, MGC17330, CD164L1, REPS1, ACHE, ITGB1BP2,LOC94431, LTK, RUNX1, EVER1, KIAA2010, CEACAM7, STX16, SLC4A5, CRTAP,RECQL5, MAGEF1, VIPR1, FLJ10979, TTC3, CRSP2, BAZ2A, GTF2I, MGC50853,KIAA0508, BPHL, LTBP4, FN3KRP, SCARB1, MGC17330, HYAL4, DGKA, FLJ11196,DHRS6, EPHB4, IDI2/GTPBP4, SNTG2, SLC7A6, PMS2L2, KIAA0436, TOSO,THRAP3, T3JAM, LOC283232, LOC92482, PTER, ATM, NUCB2, PIK3R2, MGC1136,CD59, JARID1A, FLJ39616, ABLIM1, PBP, MAPK8IP3, FTS, LHX5, TNFRSF7, MYC,PBXIP1, DATF1, HTF9C, PUS1, KIAA0924, C6orf4, KIAA0372, WDR42A, CRYZL1,TERE1, LTBP4, TTC3, NFATC1, POM121/LOC340318, TOSO,LOC348926/MGC16279/SB153/FLJ10661, SPOCK2, KIAA0515, SLC37A4, CD44,SMARCA2, SPTBN1, C6orf130, TTC3, DLG1, SLC35E2, MCCC1, PMS2L11, RCN3,STX16, FLJ20618, STAT5B, SMARCA2, SATB1, POLR1D, ASXL1, REV1L,PMS2L2/PMS2L5, FLJ12355, CCNB1IP1, FLJ12270, KIAA0692, MCM7, GPSN2,STX16, MMS19L, GTF2I/GTF2IP1, AKAP7, ZNF444, SLC35A3, MGEA5, RUTBC3,C20orf36, RAD17, ALG12, LOC112869, C6orf48, CUTC, LGTN, DEF6, WAC,HNRPH3, NS, KIAA0892, LRPPRC, HMG20A, DDX42, TINP1, ZDHHC17, C19orf2,EIF4B, LOC376745, DKFZP434C171, TH1L, C19orf13, RPL22, PHF15, EWSR1,EIF4B, FAM48A, YT521, NEK9, EIF3S7, RPS6, RPL35A, EEF2, RPL3, RPS6,UBA52, RPL6, RPS6, RPL13, AL353949, AL580863, AF052160, AW128846,AW974481, N92920, BG178274, AW303460, BF057458, AL050035, M59917,AK025422, AI693985, AU158442, AK021460, AL023773, NM_003790, AC005011,M90355, AL353580, U38964, D50683 and BE967207, wherein downregulationbelow a predetermined threshold in the level of expression relative to alevel of expression of the at least one polynucleotide in a biologicalsample of a subject diagnosed with typical relapsing-remitting multiplesclerosis (RRMS) is indicative of treatment efficacy.

According to some embodiments of the invention, step (b) is effectedalso prior to step (a) and wherein the downregulation is with respect toa level of the at least one polynucleotide prior to the treating.

According to an aspect of some embodiments of the present inventionthere is provided a method of predicting a typical relapsing-remittingmultiple sclerosis (RRMS) course in a subject diagnosed with multiplesclerosis, the method comprising: (a) determining in a biological sampleof the subject a level of expression of at least one polynucleotideselected from the group consisting of YWHAB, ATP6V1E1, UBB, MRLC2/MRCL3,UQCR, MRLC2, RTN4, UBE2A, RTN4, WDR1, PSMA6, C14orf123, PP1201, TBK1,CAST, CAST, RSN, PSME1, SDF2, GSTO1, CAST, DNCL1, SQRDL, ADIPOR2, ICMT,NDUFA6, NDUFA6, COX17, HIF1AN, FLJ20257, TBPL1, RAPGEF2, CRSP8, APOL1,PAOX, CNDP2, ETFA, DPP3, KPNA1, MGC3036, TUBB2, PDCL, CCL5, CDS2,RAP1GDS1, ATP6V1D, OBRGRP/LEPR, SF4, GCLC, MGST3, BICD2, BRF1, CHST12,EXOSC7, TOR1B, ZFP95, ILK, UNC13A, MTHFD2, CASP10, FLJ45850, CMRF-35H,ARF3, NDOR1, DUSP10, AP1M2, VRK2, GSN, PTRF, RBM19, RABGAP1L, ATP5S,STOM, TFPI2, SLCO3A1, PTPN12, CSF1, SIGLEC6, KIRREL, OBRGRP, TP53AP1,SUHW1, NUP98, IL15RA, MICB, CMRF-35H, SPHK1, TNFRSF6, FLJ11301, LRP5,STOM, EPHA2, SRC, FLJ11301, PSTPIP2, EBP, MCPH1, PTPRF, LIMK2, FSTL4,CBR1, MGC2654, MYCT1, NOL3, MITF, ATP10B, FBXO31, TBX21, LSS, SLC17A3,MNAB, CHPPR, GIF, VAMPS, ABCG2, KIF1B, LOH11CR2A, NID2, RBBP8, ETV7,CTSL, RUFY1, RSU1, PARD3, APOB, ACOX3, DAB2, LDLR, TJP2, GNAS, PARD3,NCKAP1, TAP2, HDGFRP3, LDLR, PIK3R3, HTR2B, GAS2L1, FER1L3, C3orf14,TP53TG3, LEPR, CLIC5, PDE4DIP, ATP9A, ITGB1BP1, INDO, SELP, FHL2,FER1L3, EGF, SIAT8A, HDGFRP3, LRAP, VWF, FLJ10134, IMP-3, DMN, MCTP1,FSTL1, CTNNAL1, RAB27B, THBS1, PROS1, MMRN1, CTTN, AL078596, AI148659,U00956 and M29383, wherein downregulation below a predeterminedthreshold in the level of expression relative to a level of expressionof the at least one polynucleotide in a biological sample of a subjectdiagnosed with benign multiple sclerosis (BMS) is indicative of theprediction of the relapsing-remitting multiple sclerosis course of thesubject; (b) informing the subject of the prediction of therelapsing-remitting multiple sclerosis course; thereby predicting therelapsing-remitting multiple sclerosis course in the subject diagnosedwith the multiple sclerosis.

According to an aspect of some embodiments of the present inventionthere is provided a method of predicting a typical relapsing-remittingmultiple sclerosis (RRMS) course in a subject diagnosed with multiplesclerosis, the method comprising: (a) determining in a biological sampleof the subject a level of expression of at least one polynucleotideselected from the group consisting of C22orf8, TLK1, HNRPH1, PLXDC1,TLK1, PKN2, ALS2CR8, FLJ12547, ZNF238, PDPR, NT5E, PASK, HPGD, IL6ST,JARID1A, PASK, LEF1, FLJ10246, MTUS1, FLJ14011, VSIG4, MARCH-VI,FLJ10613, EWSR1, ATP8A1, SLC4A7, FLJ21127, HNRPH1, ABLIM1, ITGA6, ADCY9,CROCC, SH3YL1, SMA4, SPTBN1, DPEP3, PDE3B, AF5Q31, NRCAM, DOCK9, IPW,FLJ20152, SIRPB2, GALNT4, CD28, TXK, ETS1, DGCR5, ZNF192, TCF7, CAMK4,SIM2, MGEA5, TGFBR2, RET, MAPK8IP3, RRN3, DKFZp547H025, FBXW11, ZNF423,DLG1, MGC17330, CD164L1, REPS1, ACHE, ITGB1BP2, LOC94431, LTK, RUNX1,EVER1, KIAA2010, CEACAM7, STX16, SLC4A5, CRTAP, RECQL5, MAGEF1, VIPR1,FLJ10979, TTC3, CRSP2, BAZ2A, GTF2I, MGC50853, KIAA0508, BPHL, LTBP4,FN3KRP, SCARB1, MGC17330, HYAL4, DGKA, FLJ11196, DHRS6, EPHB4,IDI2/GTPBP4, SNTG2, SLC7A6, PMS2L2, KIAA0436, TOSO, THRAP3, T3JAM,LOC283232, LOC92482, PTER, ATM, NUCB2, PIK3R2, MGC1136, CD59, JARID1A,FLJ39616, ABLIM1, PBP, MAPK8IP3, FTS, LHX5, TNFRSF7, MYC, PBXIP1, DATF1,HTF9C, PUS1, KIAA0924, C6orf4, KIAA0372, WDR42A, CRYZL1, TERE1, LTBP4,TTC3, NFATC1, POM121/LOC340318, TOSO, LOC348926/MGC16279/SB153/FLJ10661,SPOCK2, KIAA0515, SLC37A4, CD44, SMARCA2, SPTBN1, C6orf130, TTC3, DLG1,SLC35E2, MCCC1, PMS2L11, RCN3, STX16, FLJ20618, STAT5B, SMARCA2, SATB1,POLR1D, ASXL1, REV1L, PMS2L2/PMS2L5, FLJ12355, CCNB1IP1, FLJ12270,KIAA0692, MCM7, GPSN2, STX16, MMS19L, GTF2I/GTF2IP1, AKAP7, ZNF444,SLC35A3, MGEA5, RUTBC3, C20orf36, RAD17, ALG12, LOC112869, C6orf48,CUTC, LGTN, DEF6, WAC, HNRPH3, NS, KIAA0892, LRPPRC, HMG20A, DDX42,TINP1, ZDHHC17, C19orf2, EIF4B, LOC376745, DKFZP434C171, TH1L, C19orf13,RPL22, PHF15, EWSR1, EIF4B, FAM48A, YT521, NEK9, EIF3S7, RPS6, RPL35A,EEF2, RPL3, RPS6, UBA52, RPL6, RPS6, RPL13, AL353949, AL580863,AF052160, AW128846, AW974481, N92920, BG178274, AW303460, BF057458,AL050035, M59917, AK025422, AI693985, AU158442, AK021460, AL023773,NM_003790, AC005011, M90355, AL353580, U38964, D50683 and BE967207,wherein upregulation above a predetermined threshold in the level ofexpression relative to a level of expression of the at least onepolynucleotide in a biological sample of a subject diagnosed with benignmultiple sclerosis (BMS) is indicative of the prediction of therelapsing-remitting multiple sclerosis course of the subject; (b)informing the subject of the prediction of the relapsing-remittingmultiple sclerosis course; thereby predicting the relapsing-remittingmultiple sclerosis course in the subject diagnosed with the multiplesclerosis.

According to an aspect of some embodiments of the present inventionthere is provided a method of treating a subject diagnosed with multiplesclerosis, the method comprising: (a) determining if the subject ispredicted to have a relapsing-remitting multiple sclerosis courseaccording to the method of the invention, (b) selecting a treatmentregimen based on the prediction of the relapsing-remitting multiplesclerosis course; thereby treating the subject diagnosed with multiplesclerosis.

According to an aspect of some embodiments of the present inventionthere is provided a method of treating a subject diagnosed with multiplesclerosis, the method comprising: (a) determining in a biological sampleof the subject a level of expression of RRN3, wherein upregulation abovea predetermined threshold in the level of expression relative to a levelof expression of the RRN3 in a biological sample of a subject diagnosedwith benign multiple sclerosis (BMS) is indicative of the prediction ofthe relapsing-remitting multiple sclerosis course of the subject; (b)administering to the subject a therapeutically effective amount ofditerpenoid triepoxide Triptolide (TPT) or a derivative thereof, therebytreating the subject.

According to an aspect of some embodiments of the present inventionthere is provided a method of treating a subject diagnosed with multiplesclerosis, the method comprising: administering to the subject an agentwhich downregulates the expression level and/or activity of at least onepolynucleotide or polypeptide of the RNA polymerase 1 pathway, with theproviso that the agent is not diterpenoid triepoxide Triptolide (TPT),thereby treating the subject.

According to an aspect of some embodiments of the present inventionthere is provided a probeset comprising a plurality of oligonucleotidesand no more than 500 oligonucleotides, the plurality of oligonucleotidesspecifically recognizing the polynucleotides of C22orf8, TLK1, HNRPH1,PLXDC1, TLK1, PKN2, ALS2CR8, FLJ12547, ZNF238, PDPR, NT5E, PASK, HPGD,IL6ST, JARID1A, PASK, LEF1, FLJ10246, MTUS1, FLJ14011, VSIG4, MARCH-VI,FLJ10613, EWSR1, ATP8A1, SLC4A7, FLJ21127, HNRPH1, ABLIM1, ITGA6, ADCY9,CROCC, SH3YL1, SMA4, SPTBN1, DPEP3, PDE3B, AF5Q31, NRCAM, DOCK9, IPW,FLJ20152, SIRPB2, GALNT4, CD28, TXK, ETS1, DGCR5, ZNF192, TCF7, CAMK4,SIM2, MGEA5, TGFBR2, RET, MAPK8IP3, RRN3, DKFZp547H025, FBXW11, ZNF423,DLG1, MGC17330, CD164L1, REPS1, ACHE, ITGB1BP2, LOC94431, LTK, RUNX1,EVER1, KIAA2010, CEACAM7, STX16, SLC4A5, CRTAP, RECQL5, MAGEF1, VIPR1,FLJ10979, TTC3, CRSP2, BAZ2A, GTF2I, MGC50853, KIAA0508, BPHL, LTBP4,FN3KRP, SCARB1, MGC17330, HYAL4, DGKA, FLJ11196, DHRS6, EPHB4,IDI2/GTPBP4, SNTG2, SLC7A6, PMS2L2, KIAA0436, TOSO, THRAP3, T3JAM,LOC283232, LOC92482, PTER, ATM, NUCB2, PIK3R2, MGC1136, CD59, JARID1A,FLJ39616, ABLIM1, PBP, MAPK8IP3, FTS, LHX5, TNFRSF7, MYC, PBXIP1, DATF1,HTF9C, PUS1, KIAA0924, C6orf4, KIAA0372, WDR42A, CRYZL1, TERE1, LTBP4,TTC3, NFATC1, POM121/LOC340318, TOSO, LOC348926/MGC16279/SB153/FLJ10661,SPOCK2, KIAA0515, SLC37A4, CD44, SMARCA2, SPTBN1, C6orf130, TTC3, DLG1,SLC35E2, MCCC1, PMS2L11, RCN3, STX16, FLJ20618, STAT5B, SMARCA2, SATB1,POLR1D, ASXL1, REV1L, PMS2L2/PMS2L5, FLJ12355, CCNB1IP1, FLJ12270,KIAA0692, MCM7, GPSN2, STX16, MMS19L, GTF2I/GTF2IP1, AKAP7, ZNF444,SLC35A3, MGEA5, RUTBC3, C20orf36, RAD17, ALG12, LOC112869, C6orf48,CUTC, LGTN, DEF6, WAC, HNRPH3, NS, KIAA0892, LRPPRC, HMG20A, DDX42,TINP1, ZDHHC17, C19orf2, EIF4B, LOC376745, DKFZP434C171, TH1L, C19orf13,RPL22, PHF15, EWSR1, EIF4B, FAM48A, YT521, NEK9, EIF3S7, RPS6, RPL35A,EEF2, RPL3, RPS6, UBA52, RPL6, RPS6, RPL13, AL353949, AL580863,AF052160, AW128846, AW974481, N92920, BG178274, AW303460, BF057458,AL050035, M59917, AK025422, AI693985, AU158442, AK021460, AL023773,NM_003790, AC005011, M90355, AL353580, U38964, D50683, BE967207, YWHAB,ATP6V1E1, UBB, MRLC2/MRCL3, UQCR, MRLC2, RTN4, UBE2A, RTN4, WDR1, PSMA6,C14orf123, PP1201, TBK1, CAST, CAST, RSN, PSME1, SDF2, GSTO1, CAST,DNCL1, SQRDL, ADIPOR2, ICMT, NDUFA6, NDUFA6, COX17, HIF1AN, FLJ20257,TBPL1, RAPGEF2, CRSP8, APOL1, PAOX, CNDP2, ETFA, DPP3, KPNA1, MGC3036,TUBB2, PDCL, CCL5, CDS2, RAP1GDS1, ATP6V1D, OBRGRP/LEPR, SF4, GCLC,MGST3, BICD2, BRF1, CHST12, EXOSC7, TOR1B, ZFP95, ILK, UNC13A, MTHFD2,CASP10, FLJ45850, CMRF-35H, ARF3, NDOR1, DUSP10, AP1M2, VRK2, GSN, PTRF,RBM19, RABGAP1L, ATP5S, STOM, TFPI2, SLCO3A1, PTPN12, CSF1, SIGLEC6,KIRREL, OBRGRP, TP53AP1, SUHW1, NUP98, IL15RA, MICB, CMRF-35H, SPHK1,TNFRSF6, FLJ11301, LRP5, STOM, EPHA2, SRC, FLJ11301, PSTPIP2, EBP,MCPH1, PTPRF, LIMK2, FSTL4, CBR1, MGC2654, MYCT1, NOL3, MITF, ATP10B,FBXO31, TBX21, LSS, SLC17A3, MNAB, CHPPR, GIF, VAMPS, ABCG2, KIF1B,LOH11CR2A, NID2, RBBP8, ETV7, CTSL, RUFY1, RSU1, PARD3, APOB, ACOX3,DAB2, LDLR, TJP2, GNAS, PARD3, NCKAP1, TAP2, HDGFRP3, LDLR, PIK3R3,HTR2B, GAS2L1, FER1L3, C3orf14, TP53TG3, LEPR, CLIC5, PDE4DIP, ATP9A,ITGB1BP1, INDO, SELP, FHL2, FER1L3, EGF, SIAT8A, HDGFRP3, LRAP, VWF,FLJ10134, IMP-3, DMN, MCTP1, FSTL1, CTNNAL1, RAB27B, THBS1, PROS1,MMRN1, CTTN, AL078596, AI148659, U00956 and M29383.

According to an aspect of some embodiments of the present inventionthere is provided a kit for predicting a benign or relapsing-remittingcourse in a subject diagnosed with multiple sclerosis, comprising theprobeset of the invention.

According to some embodiments of the invention, the kit furthercomprising a positive control for an expression level of at least one ofthe polynucleotides.

According to some embodiments of the invention, the at least onepolynucleotide comprises the polynucleotides of RRN3, POLR1D and LRPPRC.

According to some embodiments of the invention, the treatment regimencomprises administering to the subject an agent which downregulates theexpression level and/or activity of at least one polynucleotide orpolypeptide of the RNA polymerase 1 pathway, thereby treating thesubject.

According to some embodiments of the invention, the at least onepolynucleotide or polypeptide of the RNA polymerase 1 pathway comprisesRRN3.

According to some embodiments of the invention, the at least onepolynucleotide or polypeptide of the RNA polymerase 1 pathway furthercomprises POLR1D and LRPPRC.

According to some embodiments of the invention, the method furthercomprising determining in the biological sample of the subject the levelof expression of POLR1D and/or LRPPRC, wherein upregulation above apredetermined threshold in the level of expression relative to a levelof expression of the POLR1D and/or LRPPRC in a biological sample of asubject diagnosed with benign multiple sclerosis (BMS) is indicative ofthe prediction of the relapsing-remitting multiple sclerosis course ofthe subject.

Unless otherwise defined, all technical and/or scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which the invention pertains. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of embodiments of the invention, exemplarymethods and/or materials are described below. In case of conflict, thepatent specification, including definitions, will control. In addition,the materials, methods, and examples are illustrative only and are notintended to be necessarily limiting.

Implementation of the method and/or system of embodiments of theinvention can involve performing or completing selected tasks manually,automatically, or a combination thereof. Moreover, according to actualinstrumentation and equipment of embodiments of the method and/or systemof the invention, several selected tasks could be implemented byhardware, by software or by firmware or by a combination thereof usingan operating system.

For example, hardware for performing selected tasks according toembodiments of the invention could be implemented as a chip or acircuit. As software, selected tasks according to embodiments of theinvention could be implemented as a plurality of software instructionsbeing executed by a computer using any suitable operating system. In anexemplary embodiment of the invention, one or more tasks according toexemplary embodiments of method and/or system as described herein areperformed by a data processor, such as a computing platform forexecuting a plurality of instructions. Optionally, the data processorincludes a volatile memory for storing instructions and/or data and/or anon-volatile storage, for example, a magnetic hard-disk and/or removablemedia, for storing instructions and/or data. Optionally, a networkconnection is provided as well. A display and/or a user input devicesuch as a keyboard or mouse are optionally provided as well.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING(S)

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

Some embodiments of the invention are herein described, by way ofexample only, with reference to the accompanying drawings. With specificreference now to the drawings in detail, it is stressed that theparticulars shown are by way of example and for purposes of illustrativediscussion of embodiments of the invention. In this regard, thedescription taken with the drawings makes apparent to those skilled inthe art how embodiments of the invention may be practiced.

In the drawings:

FIG. 1 is a schematic illustration depicting the design of the study foridentification of genes which predict benign multiple sclerosis;

FIG. 2 depicts Principal Component Analysis (PCA) based on 406 mostinformative genes (MIGs);

DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

The present invention, in some embodiments thereof, relates to methodsof classifying a subject as being more likely to have BMS or to be morelikely to have typical RRMS and, more particularly, but not exclusively,to methods of diagnosing typical RRMS or BMS and treating a subjectbased on the diagnosis.

Before explaining at least one embodiment of the invention in detail, itis to be understood that the invention is not necessarily limited in itsapplication to the details set forth in the following description orexemplified by the Examples. The invention is capable of otherembodiments or of being practiced or carried out in various ways.

The present inventors have applied a high throughput gene expressiontechnology to identify biomarkers for the diagnosis of benign multiplesclerosis (BMS) and for potential targets for therapeutic interventionsin order switch RRMS course of disease to a BMS course of disease.

Thus, as shown in Example 1 of the Examples section which follows, thepresent inventors have identified 406 genes which are differentiallyexpressed between multiple sclerosis subjects having a benign MS courseor an RRMS course (typical RRMS) (Tables 1 and 2). These genes can beused for classification of MS disease course, diagnosis of a typicalRRMS course and selecting a suitable treatment regimen for a subjectdiagnosed with MS which will prevent deterioration in the subject'sstate while avoiding unnecessary side effects. In addition, as shown inTable 3 (Example 1) and Tables 4A-C (Example 2) the present inventorshave uncovered that the expression level of genes which are involved inthe RNA polymerase I pathway such as POLR1D, LRPPRC, RRN3 and NCL isdownregulated in subjects having a BMS course of MS as compared to theexpression level of these genes in subjects having an RRMS course of MS.Moreover, as shown in Tables 5 and 6 (Example 2) the present inventorsidentified MIGs (most informative genes) discriminating between BMS andtypical RRMS and genes which can classify subjects as having a BMS or atypical RRMS. These results suggest the use of genes involved in the RNApolymerase I pathway as diagnostic markers and drug targets for treatingand preventing a typical RRMS course in a subject diagnosed with MS.

Thus, according to an aspect of some embodiments of the invention thereis provided a method of classifying a subject as being more likely tohave benign multiple sclerosis (BMS) or as being more likely to havetypical relapsing remitting multiple sclerosis (RRMS), the methodcomprising comparing a level of expression of at least one gene involvedin the RNA polymerase I pathway in a cell of the subject to a referenceexpression data of the at least one gene obtained from a cell of atleast one subject pre-diagnosed as having BMS and/or from a cell of atleast one subject pre-diagnosed as having typical RRMS, therebyclassifying the subject as being more likely to have BMS or as beingmore likely to have typical RRMS.

The term “subject” refers to mammal, preferably a human being.

According to some embodiments of the invention, the subject is diagnosedwith multiple sclerosis.

As used herein, the phrase “diagnosed with multiple sclerosis” refers toa subject who experienced at least one neurological attack affecting thecentral nervous system (CNS) accompanied by demyelinating lesions withinthe brain or spinal cord, which may have, but not necessarily confirmedby magnetic resonance imaging (MRI). The neurological attack can involveacute or sub-acute neurological symptomatology (attack) manifested byvarious clinical presentations like unilateral loss of vision, vertigo,ataxia, incoordination, gait difficulties, sensory impairmentcharacterized by paresthesia, dysesthesia, sensory loss, urinarydisturbances until incontinence, diplopia, dysarthria, various degreesof motor weakness until paralysis, cognitive decline either as amonosymptomatic or in combination. The symptoms usually remain forseveral days to few weeks, and then partially or completely resolve.

The accepted diagnostic criteria of multiple sclerosis are presented inHypertext Transfer Protocol://World Wide Web (dot) mult-sclerosis (dot)org/DiagnosticCriteria (dot) html.

According to some embodiments of the invention, the subject is suspectedof having multiple sclerosis.

According to some embodiments of the invention, the subject has probablemultiple sclerosis.

According to some embodiments of the invention, the subject does nothave a primary progressive course (PPMS).

According to some embodiments of the invention, the subject does nothave a secondary progressive MS course (SPMS).

As used herein the term “classifying” refers to determining if thesubject is more likely to have benign multiple sclerosis (BMS) ortypical relapsing remitting multiple sclerosis (RRMS).

As used herein the phrase “being more likely to have” refers to havingincreased probability to have a certain disease course (classificationof disease) than another disease course.

According to some embodiments of the invention, the phrase “being morelikely to have” refers to a probability of at least about 51%, at leastabout 52%, at least about 53%, at least about 54%, at least about 55%,at least about 56%, at least about 57%, at least about 58%, at leastabout 59%, at least about 60%, at least about 61%, at least about 62%,at least about 63%, at least about 64%, at least about 65%, at leastabout 66%, at least about 67%, at least about 68%, at least about 69%,at least about 70%, at least about 71%, at least about 72%, at leastabout 73%, at least about 74%, at least about 75%, at least about 76%,at least about 77%, at least about 78%, at least about 79%, at leastabout 80%, at least about 81%, at least about 82%, at least about 83%,at least about 84%, at least about 85%, at least about 86%, at leastabout 87%, at least about 88%, at least about 89%, at least about 90%,at least about 91%, at least about 92%, at least about 93%, at leastabout 94%, at least about 95%, at least about 96%, at least about 97%,at least about 98%, at least about 99%, e.g., about 100% that thesubject has a certain disease course and not the other disease course,i.e., a BMS or typical RRMS.

As used herein, the phrase “benign multiple sclerosis” refers to asubject having MS and exhibiting an Expanded Disability Status Scale(EDSS) of less than 3.0 following at least 10 years from onset and/ordiagnosis of MS.

As used herein, the phrase “typical RRMS” or a “relapsing-remittingmultiple sclerosis course”, which is interchangeably used herein, refersto a subject having MS and exhibiting an Expanded Disability StatusScale (EDSS) higher than 3.0 within less than 10 years of disease onsetand/or diagnosis.

The phrase “onset of multiple sclerosis (MS)” as used herein refers tothe time of occurrence of the first clinical neurological symptomatologysuggestive of MS.

The Kurtzke EDSS is a method scale of quantifying disability in MS byscoring eight Functional Systems (FS) (pyramidal, cerebellar, brainstem,sensory, bowel and bladder, visual, cerebral, and other) and allowsneurologists to assign a Functional System Score (FSS) in each and tocombine the FSS scores into the EDSS score as follows:

EDSS 0.0—Normal neurological examination;

EDSS 1.0—No disability, minimal signs in one FS;

EDSS 1.5—No disability, minimal signs in more than one FS;

EDSS 2.0—Minimal disability in one FS;

EDSS 2.5—Mild disability in one FS or minimal disability in two FS;

EDSS 3.0—Moderate disability in one FS, or mild disability in three orfour FS. Fully ambulatory;

EDSS 3.5—Fully ambulatory but with moderate disability in one FS andmore than minimal disability in several others;

EDSS 4.0—Fully ambulatory without aid, self-sufficient, up and aboutsome 12 hours a day despite relatively severe disability; able to walkwithout aid or rest some 500 meters;

EDSS 4.5—Fully ambulatory without aid, up and about much of the day,able to work a full day, may otherwise have some limitation of fullactivity or require minimal assistance; characterized by relativelysevere disability; able to walk without aid or rest some 300 meters;

EDSS 5.0—Ambulatory without aid or rest for about 200 meters; disabilitysevere enough to impair full daily activities (work a full day withoutspecial provisions);

EDSS 5.5—Ambulatory without aid or rest for about 100 meters; disabilitysevere enough to preclude full daily activities;

EDSS 6.0—Intermittent or unilateral constant assistance (cane, crutch,brace) required to walk about 100 meters with or without resting;

EDSS 6.5—Constant bilateral assistance (canes, crutches, braces)required to walk about 20 meters without resting;

EDSS 7.0—Unable to walk beyond approximately five meters even with aid,essentially restricted to wheelchair; wheels self in standard wheelchairand transfers alone; up and about in wheelchair some 12 hours a day;

EDSS 7.5—Unable to take more than a few steps; restricted to wheelchair;may need aid in transfer; wheels self but cannot carry on in standardwheelchair a full day, May require motorized wheelchair;

EDSS 8.0—Essentially restricted to bed or chair or perambulated inwheelchair, but may be out of bed itself much of the day; retains manyself-care functions; generally has effective use of arms;

EDSS 8.5—Essentially restricted to bed much of day, has some effectiveuse of arms retains some self care functions;

EDSS 9.0—Confined to bed; can still communicate and eat;

EDSS 9.5—Totally helpless bed patient; unable to communicate effectivelyor eat/swallow;

EDSS 10.0—Death due to MS;

As mentioned, the diagnosis of MS is performed by clinical neurologicalsymptoms and/or findings such as laboratory tests involving evaluationof IgG synthesis and oligoclonal bands (immunoglobulins) in thecerebrospinal fluid (CSF) which provide evidence of chronic inflammationof the central nervous system, and brain or spinal cord MRI according tothe McDonald criteria [McDonald W I, Compston A, Edan G, et al., 2001,“Recommended diagnostic criteria for multiple sclerosis: guidelines fromthe International Panel on the diagnosis of multiple sclerosis”. AnnNeurol. 50 (1): 121-7; Polman C H, Reingold S C, Edan G, et al., 2005,“Diagnostic criteria for multiple sclerosis: 2005 revisions to the“McDonald Criteria””. Ann Neurol. 58 (6): 840-6].

It should be noted that onset of multiple sclerosis and the diagnosis ofmultiple sclerosis could occur on the same time.

As used herein, the phrase “level of expression” refers to the degree ofgene expression and/or gene product activity in a specific cell. Forexample, up-regulation or down-regulation of various genes can affectthe level of the gene product (i.e., RNA and/or protein) in a specificcell.

Sequence information regarding gene products (i.e., RNA transcripts andpolypeptide sequences) of the genes of the polynucleotides of theinvention such as the genes of RNA polymerase I pathway and of probeswhich can be used to detect thereof can be found in Tables 1, 2, 3, 5and 6 of the Examples section which follows.

It should be noted that the level of expression can be determined inarbitrary absolute units, or in normalized units (relative to knownexpression levels of a control reference). For example, when using DNAchips, the expression levels are normalized according to the chips'internal controls or by using quantile normalization such as RMA.

As used herein the phrase “a cell of the subject” refers to at least onecell (e.g., an isolated cell), cell culture, cell content and/or cellsecreted content which contains RNA and/or proteins of the subject.Examples include a blood cell, a cell obtained from any tissue biopsy[e.g., cerebrospinal fluid, (CSF), brain biopsy], a bone marrow cell,body fluids such as plasma, serum, saliva, spinal fluid, lymph fluid,the external sections of the skin, respiratory, intestinal, andgenitourinary tracts, tears, saliva, sputum and milk. According to anembodiment of the invention, the cell is a blood cell (e.g., white bloodcells, macrophages, B- and T-lymphocytes, monocytes, neutrophiles,eosinophiles, and basophiles) which can be obtained using a syringeneedle from a vein of the subject. It should be noted that the cell maybe isolated from the subject (e.g., for in vitro detection) or mayoptionally comprise a cell that has not been physically removed from thesubject (e.g., in vivo detection).

According to some embodiments of the invention, the white blood cellcomprises peripheral blood mononuclear cells (PBMC). The phrase,“peripheral blood mononuclear cells (PBMCs)” as used herein, refers to amixture of monocytes and lymphocytes. Several methods for isolatingwhite blood cells are known in the art. For example, PBMCs can beisolated from whole blood samples using density gradient centrifugationprocedures. Typically, anticoagulated whole blood is layered over theseparating medium. At the end of the centrifugation step, the followinglayers are visually observed from top to bottom: plasma/platelets,PBMCs, separating medium and erythrocytes/granulocytes. The PBMC layeris then removed and washed to remove contaminants (e.g., red bloodcells) prior to determining the expression level of thepolynucleotide(s) therein.

The cell or the biological sample comprising same can be obtained fromthe subject at any time, e.g., immediately after an attack or at anytime during remission.

According to some embodiments of the invention, the level of expressionof the gene(s) of the invention is determined using an RNA and/or aprotein detection method.

According to some embodiments of the invention, the RNA or proteinmolecules are extracted from the cell of the subject.

Methods of extracting RNA or protein molecules from cells of a subjectare well known in the art. Once obtained, the RNA or protein moleculescan be characterized for the expression and/or activity level of variousRNA and/or protein molecules using methods known in the arts.

Non-limiting examples of methods of detecting RNA molecules in a cellsample include Northern blot analysis, RT-PCR, RNA in situ hybridization(using e.g., DNA or RNA probes to hybridize RNA molecules present in thecells or tissue sections), in situ RT-PCR (e.g., as described in Nuovo GJ, et al. Am J Surg Pathol. 1993, 17: 683-90; Komminoth P, et al. PatholRes Pract. 1994, 190: 1017-25), and oligonucleotide microarray (e.g., byhybridization of polynucleotide sequences derived from a sample tooligonucleotides attached to a solid surface [e.g., a glass wafer) withaddressable location, such as Affymetrix microarray (Affymetrix®, SantaClara, Calif.)].

For example, the level of RRN3 in a sample can be determined by RT-PCRusing primers available from Santa Cruz Biotechnology Inc.(sc-106866-PR), or Taqman Gene Expression Assay HS00607907_ml (AppliedBiosystems, Foster City, Calif., USA), according to manufacturer'srecommendation.

Non-limiting examples of methods of detecting the level and/or activityof specific protein molecules in a cell sample include Enzyme linkedimmunosorbent assay (ELISA), Western blot analysis, radio-immunoassay(RIA), Fluorescence activated cell sorting (FACS), immunohistochemicalanalysis, in situ activity assay (using e.g., a chromogenic substrateapplied on the cells containing an active enzyme), in vitro activityassays (in which the activity of a particular enzyme is measured in aprotein mixture extracted from the cells). For example, in case thedetection of the expression level of a secreted protein is desired,ELISA assay may be performed on a sample of fluid obtained from thesubject (e.g., serum), which contains cell-secreted content.

As used herein the phrase “reference expression data” refers to theexpression level of the gene in a cell of at least one subject who ispre-diagnosed as having BMS or typical RRMS. Such as an expression levelcan be known from the literature, from the database, or from biologicalsamples comprising RNA or protein molecules obtained from a referencesubject who is already diagnosed as having BMS or typical RRMS.

As used herein the phrase “pre-diagnosed” refers to being diagnosedbased on the acceptable clinical tools/markers as described above (e.g.,by evaluating the EDSS score after 10 years from onset or diagnosis ofMS).

According to some embodiments of the invention, the reference expressiondata is obtained from at least subject who is pre-diagnosed as havingBMS, e.g., from at least 2, from at least 3, from at least 4, from atleast 5, from at least 6, from at least 7, from at least 8, from atleast 9, from at least 10, from at least 20, from at least 30, from atleast 40, from at least 50, from at least 100 or more subjects who arepre-diagnosed as having BMS.

According to some embodiments of the invention, the reference expressiondata is obtained from at least one subject who is pre-diagnosed ashaving typical RRMS, e.g., from at least 2, from at least 3, from atleast 4, from at least 5, from at least 6, from at least 7, from atleast 8, from at least 9, from at least 10, from at least 20, from atleast 30, from at least 40, from at least 50, from at least 100 or moresubjects who are pre-diagnosed as having typical RRMS.

It should be noted that when more than one reference subjects (i.e., asubject who is pre-diagnosed as having BMS or typical RRMS) is used, thereference expression data may comprise an average of the expressionlevel of several or all subjects, and those of skills in the art arecapable of averaging expression levels from 2 or more subject, usinge.g., normalized expression values.

According to some embodiments of the invention, a decrease above apredetermined threshold in the level of expression of the at least onegene in the cell of the subject relative to the reference expressiondata of the at least one gene obtained from a cell of the at least onesubject having the typical RRMS classifies the subject as being morelikely to have the BMS.

As used herein the phrase “a decrease above a predetermined threshold”refers to a decrease in the level of expression in the cell of thesubject relative to the reference expression data obtained from a cellof the at least one subject having the typical RRMS which is higher thana predetermined threshold such as a about 10%, e.g., higher than about20%, e.g., higher than about 30%, e.g., higher than about 40%, e.g.,higher than about 50%, e.g., higher than about 60%, higher than about70%, higher than about 80%, higher than about 90%, higher than about 2times, higher than about three times, higher than about four time,higher than about five times, higher than about six times, higher thanabout seven times, higher than about eight times, higher than about ninetimes, higher than about 20 times, higher than about 50 times, higherthan about 100 times, higher than about 200 times, higher than about350, higher than about 500 times, higher than about 1000 times, or morerelative to the reference expression data obtained from a cell of the atleast subject having the typical RRMS.

According to some embodiments of the invention, an increase above apredetermined threshold in the level of expression of the at least onegene in the cell of the subject relative to the reference expressiondata of the at least one gene obtained from a cell of the at least onesubject having the BMS classifies the subject as being more likely tohave the typical RRMS.

As used herein the phrase “an increase above a predetermined threshold”refers to an increase in the level of expression in the cell of thesubject relative to the reference expression data obtained from a cellof the at least one subject having the BMS which is higher than apredetermined threshold such as a about 10%, e.g., higher than about20%, e.g., higher than about 30%, e.g., higher than about 40%, e.g.,higher than about 50%, e.g., higher than about 60%, higher than about70%, higher than about 80%, higher than about 90%, higher than about 2times, higher than about three times, higher than about four time,higher than about five times, higher than about six times, higher thanabout seven times, higher than about eight times, higher than about ninetimes, higher than about 20 times, higher than about 50 times, higherthan about 100 times, higher than about 200 times, higher than about350, higher than about 500 times, higher than about 1000 times, or morerelative to the reference expression data obtained from a cell of the atleast one subject having the BMS.

According to some embodiments of the invention, when a level ofexpression of the at least one gene in the cell of the subject isidentical or changed below a predetermined threshold as compared to thereference expression data of the at least one gene obtained from a cellof the at least one subject having the BMS, then the subject isclassified as being more likely to have the BMS.

As used herein the phrase “changed below a predetermined threshold ascompared to the reference expression data . . . subject having the BMS”refers to an increase or a decrease in the level of expression in thecell of the subject relative to the reference expression data obtainedfrom a cell of the at least one subject having the BMS which is lowerthan a predetermined threshold, such as lower than about 10 times, e.g.,lower than about 9 times, e.g., lower than about 8 times, e.g., lowerthan about 7 times, e.g., lower than about 6 times, e.g., lower thanabout 5 times, e.g., lower than about 4 times, e.g., lower than about 3times, e.g., lower than about 2 times, e.g., lower than about 90%, e.g.,lower than about 80%, e.g., lower than about 70%, e.g., lower than about60%, e.g., lower than about 50%, e.g., lower than about 40%, e.g., lowerthan about 30%, e.g., lower than about 20%, e.g., lower than about 10%,e.g., lower than about 9%, e.g., lower than about 8%, e.g., lower thanabout 7%, e.g., lower than about 6%, e.g., lower than about 5%, e.g.,lower than about 4%, e.g., lower than about 3%, e.g., lower than about2%, e.g., lower than about 1% relative to the reference expression dataobtained from a cell of the at least one subject having the BMS.

According to some embodiments of the invention, when a level ofexpression of the at least one gene in the cell of the subject isidentical or changed below a predetermined threshold as compared to thereference expression data of the at least one gene obtained from a cellof the at least one subject having the typical RRMS, then the subject isclassified as being more likely to have the typical RRMS.

As used herein the phrase “changed below a predetermined threshold ascompared to the reference expression data . . . subject having thetypical RRMS” refers to an increase or a decrease in the level ofexpression in the cell of the subject relative to the referenceexpression data obtained from a cell of the one subject having thetypical RRMS which is lower than a predetermined threshold, such aslower than about 10 times, e.g., lower than about 9 times, e.g., lowerthan about 8 times, e.g., lower than about 7 times, e.g., lower thanabout 6 times, e.g., lower than about 5 times, e.g., lower than about 4times, e.g., lower than about 3 times, e.g., lower than about 2 times,e.g., lower than about 90%, e.g., lower than about 80%, e.g., lower thanabout 70%, e.g., lower than about 60%, e.g., lower than about 50%, e.g.,lower than about 40%, e.g., lower than about 30%, e.g., lower than about20%, e.g., lower than about 10%, e.g., lower than about 9%, e.g., lowerthan about 8%, e.g., lower than about 7%, e.g., lower than about 6%,e.g., lower than about 5%, e.g., lower than about 4%, e.g., lower thanabout 3%, e.g., lower than about 2%, e.g., lower than about 1% relativeto the reference expression data obtained from the at least one subjecthaving the typical RRMS.

Non-limiting examples of genes involved in the RNA polymerase I pathwaywhich can be used according to the method of the invention are providedin Table 3 along with representative polynucleotides thereof and probeswhich can be used to detect thereof (Example 1 of the Examples sectionwhich follows; e.g., RRN3, LRPPRC, POLR1B, POLR1C, POLR1D, POLR2A,POLR2B, POLR2C, POLR2D, POLR2E, POLR2E, POLR2F, POLR2G, POLR2H, POLR2I,POLR2J, POLR2J2, MGC13098, POLR2K, POLR2L, POLR3B, POLR3C, POLR3D,POLR3E, POLR3F, POLR3G, POLR3K, POLRMT, POLRMT and POLS).

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway is selected from the groupconsisting of POLR1D, LRPPRC, RRN3 and NCL.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway is RRN3.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway is LRPPRC.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway is POLR1D.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway comprises RRN3 and POLR1D.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway comprises RRN3 and LRPPRC.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway comprises POLR1D and LRPPRC.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway comprises RRN3, LRPPRC andPOLR1D.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway is RRN3 and NCL.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway is LRPPRC and NCL.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway is POLR1D and NCL.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway comprises RRN3, POLR1D and NCL.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway comprises RRN3, LRPPRC and NCL.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway comprises POLR1D, LRPPRC andNCL.

According to some embodiments of the invention, the at least one geneinvolved in the RNA polymerase 1 pathway comprises RRN3, LRPPRC, POLR1Dand NCL.

Tables 4A-C in the Examples section which follows demonstrate exemplarycombinations of genes of the RNA polymerase I pathway along with theirclassification rates for BMS and typical RRMS.

The prediction of the MS course is important in terms of monitoring theclinical state of the subject (e.g., how often does the patient need tobe evaluated for the disease progression in terms of neurologicalevaluation and EDSS), planning of subject's future life (e.g., makingdecisions regarding marriage, having children, being involved in highrisk activities, getting a life-insurance, etc.) and planning thetreatment regimen of the subject.

For example, a subject who is more likely to have BMS may be advised toreduce the frequency of neurological clinical evaluations to no morethan once per year; to avoid frequent MRI examinations; to not beincluded in treatment schedule of MS; and/or to avoid receivingimmunomodulatory drugs which have side effects or adverse events thatcan be even life-threatening [e.g., progressive multifocalleukoencephalopathy (PML) in MS patients treated with natalizumab(Tysabri®, Biogen-Idec); Hypertext Transfer Protocol://World Wide Web(dot) va (dot) gov/MS/pressreleases/Treating_Natalizumab_and_Risk_of_PML(dot) asp].

On the other hand, a subject who is more likely to have typical RRMS maybe advised to have neurological clinical evaluations at a higherfrequency, e.g., about 3-4 times per year; to have frequent MRIexaminations; to be included in treatment schedule of MS; and/or toreceive immunomodulatory drugs.

It should be noted that the classification of the subject as being morelikely to have BMS or typical RRMS can be used to diagnose the subjectas having BMS or typical RRMS.

As used herein the term “diagnosing” refers to determining presence orabsence of a pathology (e.g., a disease, disorder, condition orsyndrome) and/or likelihood of same, classifying a pathology or asymptom, determining a severity of the pathology, monitoring pathologyprogression, forecasting an outcome of a pathology and/or prospects ofrecovery and screening of a subject for a specific disease.

According to some embodiments of the invention the method of diagnosingis effected by (a) classifying the subject as being more likely to haveBMS or as being more likely to have typical RRMS according to the methodof the invention,

(i) wherein when the subject is classified as being more likely to havethe BMS then the subject is diagnosed as having BMS;

(ii) wherein when the subject is classified as being more likely to havethe typical RRMS, then the subject is diagnosed as having typical RRMS;and

(c) informing the subject of the diagnosis,

thereby diagnosing the subject pre-diagnosed with the MS as having theBMS or the typical RRMS.

According to some embodiments of the invention, the subject ispre-diagnosed with multiple sclerosis (MS), i.e., has a confirmeddiagnosis of MS without knowing the disease course, e.g., typical RRMS,BMS.

As used herein the term “informing” refers to providing to the subjectthe results of the diagnosis of the disease sub-class (i.e., BMS ortypical RRMS). The results may be provided as a computer output and/ororal conversation with the subject.

The teachings of the invention can be also used to determine efficiencyanti multiple sclerosis drugs by determining the effect of the drug(s)on the expression level of the at least one gene of the RNA polymerase Ipathway.

Thus, according to an aspect of some embodiments of the invention, thereis provided a method of monitoring an efficiency of an anti multiplesclerosis (MS) drug in treating a subject diagnosed with a typicalrelapsing remitting multiple sclerosis (RRMS) course, the method iseffected by:

(a) treating the subject with the anti MS drug; and

(b) comparing a level of expression of least one gene involved in theRNA polymerase I pathway in a cell of the subject following treatingwith the anti MS drug to a level of expression of the at least one genein a cell of the subject prior to the treating the subject with the antiMS drug,

(i) wherein a decrease above a predetermined threshold in the level ofexpression of the at least one gene following the treating with the antiMS drug relative to the level of expression of the at least one geneprior to the treating with the anti MS drug indicates that the anti MSdrug is efficient for treating the subject;

(ii) wherein an increase above a predetermined threshold in the level ofexpression of the at least one gene following the treating with the antiMS drug relative to the level of expression of the at least one geneprior to the treating with the anti MS drug indicates that the anti MSdrug is not efficient for treating the subject; or

(iii) wherein when a level of expression of the at least one genefollowing the treating with the anti MS drug is identical or changedbelow a predetermined threshold as compared to prior to the treatingwith the anti MS drug then the treatment is not efficient for treatingthe subject.

thereby monitoring the efficiency of the anti multiple sclerosis (MS)drug in treating the subject diagnosed with the typical RRMS course.

As used herein the phrase “treating” refers to inhibiting or arrestingthe development of pathology [multiple sclerosis, e.g., typical RRMS]and/or causing the reduction, remission, or regression of a pathologyand/or optimally curing the pathology. Those of skill in the art willunderstand that various methodologies and assays can be used to assessthe development of pathology, and similarly, various methodologies andassays may be used to assess the reduction, remission or regression ofthe pathology.

According to some embodiments of the invention, treating the subjectrefers to changing the disease course of the subject from a typical RRMScourse to a BMS course.

According to some embodiments of the invention, treating the subjectrefers to preventing a typical RRMS course.

As used herein the phrase “following treating with the anti MS drug”refers to any time period after administering the anti MS drug to thesubject, e.g., from a few minutes to hours, or from a few days to weeksor months after drug administration.

According to some embodiments of the invention the level of expressionis determined following the first dose of the anti MS drug.

According to some embodiments of the invention the level of expressionis determined following any dose of the anti MS drug.

As used herein the phrase “prior to treating with the anti MS drug”refers to any time period prior administering the anti MS drug to thesubject, e.g., from a few minutes to hours, or from a few days to weeksor months prior to drug administration.

According to some embodiments of the invention the level of expressionis determined prior any dose of the anti MS drug (e.g., when the subjectis naïve to treatment).

According to some embodiments of the invention prior to treating refersto when the subject is first diagnosed with multiple sclerosis.

According to some embodiments of the invention prior to treating refersto when the subject is suspected of having multiple sclerosis, ordiagnosed with probable multiple sclerosis.

According to some embodiments of the invention prior to treating refersto upon MS disease onset.

According to some embodiments of the invention the effect of thetreatment on the subject can be evaluated by monitoring the level ofexpression of at least one of the polynucleotides described hereinabove.For example, downregulation in the level of RRN3 in the subjectfollowing treatment can be indicative of the positive effect of thetreatment on the subject, i.e., switching from a typical RRMS to a BMScourse of disease.

The teachings of the invention can be also used to predict efficiency ofa drug in vitro.

Thus, according to an aspect of some embodiments of the invention thereis provided an in vitro method of predicting an efficiency of an antimultiple sclerosis (MS) drug for treatment of a subject diagnosed with atypical relapsing remitting multiple sclerosis (RRMS), the method iseffected by:

(a) contacting cells of the subject with a therapeutically effectiveamount of the anti MS drug; and

(b) comparing a level of expression in the cells of at least one geneinvolved in the RNA polymerase I pathway following the contacting withthe anti MS drug to a level of expression of the at least one gene inthe cells prior to the contacting with the anti MS drug,

(i) wherein a decrease above a predetermined threshold in the level ofexpression of the at least one gene following the contacting with theanti MS drug relative to the level of expression of the at least onegene prior to the contacting with the anti MS drug indicates that thetreatment is efficient for treating the subject;

(ii) wherein an increase above a predetermined threshold in the level ofexpression of the at least one gene following the contacting with theanti MS drug relative to the level of expression of the at least onegene prior to the contacting with the anti MS drug indicates that thetreatment is not efficient for treating the subject; or

(iii) wherein when a level of expression of the at least one genefollowing the contacting with the anti MS drug is identical or changedbelow a predetermined threshold as compared to prior to the contactingwith the anti MS drug then the treatment is not efficient for treatingthe subject.

thereby predicting the efficiency of the anti MS drug for treatment ofthe subject diagnosed with the typical RRMS.

Contacting cells with the anti MS drug can be performed by any in vitroconditions including for example, adding the anti MS drug to cellsderived from a subject (e.g., a primary cell culture, a cell line) or toa biological sample comprising same (e.g., a fluid, liquid whichcomprises the cells) such that the drug is in direct contact with thecells. According to some embodiments of the invention, the cells of thesubject are incubated with the anti MS drug. The conditions used forincubating the cells are selected for a time period/concentration ofcells/concentration of drug/ratio between cells and drug and the likewhich enable the drug to induce cellular changes, such as changes intranscription and/or translation rate of specific genes, proliferationrate, differentiation, cell death, necrosis, apoptosis and the like.

Methods of monitoring cellular changes induced by the drugs are known inthe art and include for example, the MTT test which is based on theselective ability of living cells to reduce the yellow salt MTT(3-(4,5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide) (Sigma,Aldrich St Louis, Mo., USA) to a purple-blue insoluble formazanprecipitate; the BrDu assay [Cell Proliferation ELISA BrdU colorimetrickit (Roche, Mannheim, Germany]; the TUNEL assay [Roche, Mannheim,Germany]; the Annexin V assay [ApoAlert® Annexin V Apoptosis Kit(Clontech Laboratories, Inc., CA, USA)]; the Senescenceassociated-β-galactosidase assay (Dimri G P, Lee X, et al. 1995. Abiomarker that identifies senescent human cells in culture and in agingskin in vivo. Proc Natl Acad Sci USA 92:9363-9367); as well as variousRNA and protein detection methods (which detect level of expressionand/or activity) which are further described hereinabove.

According to some embodiments of the invention, the cells are incubatedunder conditions which enable the effect of the drug on cellularprocesses such as downregulation of the at least one gene of the RNApolymerase I pathway.

According to an aspect of some embodiments of the invention there isprovided a method of treating a subject diagnosed with multiplesclerosis, the method is effected by: (a) classifying the subject asbeing more likely to have BMS or typical RRMS according to the method ofthe invention, (b) selecting a treatment regimen based on classificationresults of step (a); thereby treating the subject diagnosed withmultiple sclerosis.

As used herein the phrase “treatment regimen” refers to a treatment planthat specifies the type of treatment, dosage, schedule and/or durationof a treatment provided to a subject in need thereof (e.g., a subjectdiagnosed with MS). The selected treatment regimen can be an aggressiveone which is expected to result in the best clinical outcome (e.g.,complete cure of the pathology) or a more moderate one which may reliefsymptoms of the pathology yet results in incomplete cure of thepathology. It will be appreciated that in certain cases the moreaggressive treatment regimen may be associated with some discomfort tothe subject or adverse side effects (e.g., a damage to healthy cells ortissue). The dosage, schedule and duration of treatment can vary,depending on the severity of pathology and the selected type oftreatment, and those of skills in the art are capable of adjusting thetype of treatment with the dosage, schedule and duration of treatment.

For example, when the subject is classified as being more likely to havetypical RRMS (or being diagnosed with typical RRMS) then the treatmentregimen is an aggressive therapy such as an immunomodulation therapy,e.g., a high dosage of interferon beta 1a [Rebif, which can beadministered subcutaneously, at a dosage of e.g., 44 μg, three times aweek].

MS drugs which can be administered to a subject predicted to have anRRMS course of disease according to the present teachings include, butare not limited to Diterpenoid triepoxide Triptolide (TPT), Adderall;Ambien; Avonex; Baclofen; Beta interferon; Betaseron; Celexa;Clonazepam; Copaxone; Corticosteroids; Cymbalta; Cytoxan; Dexamethasone;Effexor; Elavil; Gabapentin; Hydrocodone; Lexapro; Lyrica; Mitoxantrone;Naltrexone; Neurontin; Novantrone; Prednisone; Provigil; Rebif;Solumedrol; Symmetrel; Topamax; Tysabri; Wellbutrin; Xanax; Zanaflex;Zoloft; Novartis' fingolimod [sphingosine 1-phosphate receptor (S1P-R)modulator]; Teva's laquinimod; Merck KGaA's Mylinax (cladribine);Sanofi-aventis' teriflunomide; Biogen Idec's BG-12 (Phase III);GSK/Mitsubishi Tanabe Pharma's firategrast; MediciNova's ibudilast;Biogen/UCB's CDP323 (Phase II).

One the other hand, when the subject is classified as being more likelyto have BMS (or is diagnosed with BMS) then the aggressive treatment isnot recommended, and these patients would not be treated or treatmentcan be delayed.

In addition, knowing the prediction or classification of MS diseasecourse (BMS or typical RRMS) is highly beneficial in terms of savingun-necessary costs to the health system.

According to an aspect of some embodiments of the invention there isprovided a method of treating a subject diagnosed with multiplesclerosis, the method is effected by (a) diagnosing a typical relapsingremitting multiple sclerosis (RRMS) according to the method of theinvention, and (b) administering to the subject a therapeuticallyeffective amount of diterpenoid triepoxide Triptolide (TPT) or aderivative thereof, thereby treating the subject

TPT derivatives and preparation thereof are described in WO9852933A1,which is fully incorporated herein by reference. Non-limiting examplesof TPT derivatives include, compounds of the general formulas.

Wherein

represents a single or double bond;R₁ and R₂ each independently is H or —OR₅;R3 is H, —C(═O)(CH2)nCO2H or a suitable amino acid; R, is H or —OH; R,is H, —C(═O)(CH2)nCO2H or a suitable amino acid;n is the integer 2, 3, 4, 5 or 6;and the stereoisomers, enantiomers and pharmaceutically acceptable saltsthereof; provided that R, and R2 are H when R, is other than H (forfurther details see WO9852933A1).

A commercially available preparation of Triptolide which can be usedaccording to the teachings of the invention isTrisoxireno(4b,5:6,7:8a,9)phenanthro(1,2-c)furan-1(3H)-one,3b,4,4a,6,6a,7a,7b,8b,9,10-decahydro-6-hydroxy-8b-methyl-6a-(1-methylethyl)-,(3bS,4aS,5aS,6R,6aR,7aS,7bS,8aS,8bS)-[CAS No.: 38748-32-2; PG490,Chengdu Biopurify Phytochemicals Ltd. Chengdu, Sichuan, China].

According to some embodiments of the invention, when the subject is morelikely to have typical RRMS then the treatment regimen comprisesadministering to the subject an agent which downregulates the level ofexpression of the at least one gene involved in the RNA polymerase Ipathway.

According to some embodiments of the invention, treating the subject iseffected by downregulating the expression level and/or activity (RNAand/or polypeptide encoded thereby) of at least one polynucleotide ofthe polymerase I pathway (for details see the list ofgenes/polynucleotide in Table 3 in Example 1 of the Examples sectionwhich follows).

Following is a list of downregulating agents which can decrease theexpression level of the gene product (RNA or protein molecules) of atleast one of the polynucleotides of the polymerase I pathway.

Downregulation can be effected on the genomic and/or the transcriptlevel using a variety of molecules which interfere with transcriptionand/or translation (e.g., RNA silencing agents, Ribozyme, DNAzyme andantisense), or on the protein level using e.g., an antibody,antagonists, enzymes that cleave the polypeptide and the like.

One example, of an agent capable of downregulating apolypeptide-of-interest is an antibody or antibody fragment capable ofspecifically binding the polypeptide-of-interest. Preferably, theantibody specifically binds at least one epitope of thepolypeptide-of-interest. As used herein, the term “epitope” refers toany antigenic determinant on an antigen to which the paratope of anantibody binds.

Epitopic determinants usually consist of chemically active surfacegroupings of molecules such as amino acids or carbohydrate side chainsand usually have specific three dimensional structural characteristics,as well as specific charge characteristics.

The term “antibody” as used in this invention includes intact moleculesas well as functional fragments thereof, such as Fab, F(ab′)2, and Fvthat are capable of binding to macrophages. These functional antibodyfragments are defined as follows: (1) Fab, the fragment which contains amonovalent antigen-binding fragment of an antibody molecule, can beproduced by digestion of whole antibody with the enzyme papain to yieldan intact light chain and a portion of one heavy chain; (2) Fab′, thefragment of an antibody molecule that can be obtained by treating wholeantibody with pepsin, followed by reduction, to yield an intact lightchain and a portion of the heavy chain; two Fab′ fragments are obtainedper antibody molecule; (3) (Fab′)2, the fragment of the antibody thatcan be obtained by treating whole antibody with the enzyme pepsinwithout subsequent reduction; F(ab′)2 is a dimer of two Fab′ fragmentsheld together by two disulfide bonds; (4) Fv, defined as a geneticallyengineered fragment containing the variable region of the light chainand the variable region of the heavy chain expressed as two chains; and(5) Single chain antibody (“SCA”), a genetically engineered moleculecontaining the variable region of the light chain and the variableregion of the heavy chain, linked by a suitable polypeptide linker as agenetically fused single chain molecule.

Methods of producing polyclonal and monoclonal antibodies as well asfragments thereof are well known in the art (See for example, Harlow andLane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory,New York, 1988, incorporated herein by reference).

Antibody fragments according to the present invention can be prepared byproteolytic hydrolysis of the antibody or by expression in E. coli ormammalian cells (e.g. Chinese hamster ovary cell culture or otherprotein expression systems) of DNA encoding the fragment. Antibodyfragments can be obtained by pepsin or papain digestion of wholeantibodies by conventional methods. For example, antibody fragments canbe produced by enzymatic cleavage of antibodies with pepsin to provide a5S fragment denoted F(ab′)2. This fragment can be further cleaved usinga thiol reducing agent, and optionally a blocking group for thesulfhydryl groups resulting from cleavage of disulfide linkages, toproduce 3.5S Fab′ monovalent fragments. Alternatively, an enzymaticcleavage using pepsin produces two monovalent Fab′ fragments and an Fcfragment directly. These methods are described, for example, byGoldenberg, U.S. Pat. Nos. 4,036,945 and 4,331,647, and referencescontained therein, which patents are hereby incorporated by reference intheir entirety. See also Porter, R. R. [Biochem. J. 73: 119-126 (1959)].Other methods of cleaving antibodies, such as separation of heavy chainsto form monovalent light-heavy chain fragments, further cleavage offragments, or other enzymatic, chemical, or genetic techniques may alsobe used, so long as the fragments bind to the antigen that is recognizedby the intact antibody.

Fv fragments comprise an association of VH and VL chains. Thisassociation may be noncovalent, as described in Inbar et al. [Proc.Nat'l Acad. Sci. USA 69:2659-62 (19720]. Alternatively, the variablechains can be linked by an intermolecular disulfide bond or cross-linkedby chemicals such as glutaraldehyde. Preferably, the Fv fragmentscomprise VH and VL chains connected by a peptide linker. Thesesingle-chain antigen binding proteins (sFv) are prepared by constructinga structural gene comprising DNA sequences encoding the VH and VLdomains connected by an oligonucleotide. The structural gene is insertedinto an expression vector, which is subsequently introduced into a hostcell such as E. coli. The recombinant host cells synthesize a singlepolypeptide chain with a linker peptide bridging the two V domains.Methods for producing sFvs are described, for example, by [Whitlow andFilpula, Methods 2: 97-105 (1991); Bird et al., Science 242:423-426(1988); Pack et al., Bio/Technology 11:1271-77 (1993); and U.S. Pat. No.4,946,778, which is hereby incorporated by reference in its entirety.

Another form of an antibody fragment is a peptide coding for a singlecomplementarity-determining region (CDR). CDR peptides (“minimalrecognition units”) can be obtained by constructing genes encoding theCDR of an antibody of interest. Such genes are prepared, for example, byusing the polymerase chain reaction to synthesize the variable regionfrom RNA of antibody-producing cells. See, for example, Larrick and Fry[Methods, 2: 106-10 (1991)].

Humanized forms of non-human (e.g., murine) antibodies are chimericmolecules of immunoglobulins, immunoglobulin chains or fragments thereof(such as Fv, Fab, Fab′, F(ab′).sub.2 or other antigen-bindingsubsequences of antibodies) which contain minimal sequence derived fromnon-human immunoglobulin. Humanized antibodies include humanimmunoglobulins (recipient antibody) in which residues form acomplementary determining region (CDR) of the recipient are replaced byresidues from a CDR of a non-human species (donor antibody) such asmouse, rat or rabbit having the desired specificity, affinity andcapacity. In some instances, Fv framework residues of the humanimmunoglobulin are replaced by corresponding non-human residues.Humanized antibodies may also comprise residues which are found neitherin the recipient antibody nor in the imported CDR or frameworksequences. In general, the humanized antibody will comprisesubstantially all of at least one, and typically two, variable domains,in which all or substantially all of the CDR regions correspond to thoseof a non-human immunoglobulin and all or substantially all of the FRregions are those of a human immunoglobulin consensus sequence. Thehumanized antibody optimally also will comprise at least a portion of animmunoglobulin constant region (Fc), typically that of a humanimmunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann etal., Nature, 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol.,2:593-596 (1992)].

Methods for humanizing non-human antibodies are well known in the art.Generally, a humanized antibody has one or more amino acid residuesintroduced into it from a source which is non-human. These non-humanamino acid residues are often referred to as import residues, which aretypically taken from an import variable domain. Humanization can beessentially performed following the method of Winter and co-workers[Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)], bysubstituting rodent CDRs or CDR sequences for the correspondingsequences of a human antibody. Accordingly, such humanized antibodiesare chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantiallyless than an intact human variable domain has been substituted by thecorresponding sequence from a non-human species. In practice, humanizedantibodies are typically human antibodies in which some CDR residues andpossibly some FR residues are substituted by residues from analogoussites in rodent antibodies.

Human antibodies can also be produced using various techniques known inthe art, including phage display libraries [Hoogenboom and Winter, J.Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol., 222:581(1991)]. The techniques of Cole et al. and Boerner et al. are alsoavailable for the preparation of human monoclonal antibodies (Cole etal., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77(1985) and Boerner et al., J. Immunol., 147(1):86-95 (1991)]. Similarly,human antibodies can be made by introduction of human immunoglobulinloci into transgenic animals, e.g., mice in which the endogenousimmunoglobulin genes have been partially or completely inactivated. Uponchallenge, human antibody production is observed, which closelyresembles that seen in humans in all respects, including generearrangement, assembly, and antibody repertoire. This approach isdescribed, for example, in U.S. Pat. Nos. 5,545,807; 5,545,806;5,569,825; 5,625,126; 5,633,425; 5,661,016, and in the followingscientific publications: Marks et al., Bio/Technology 10: 779-783(1992); Lonberg et al., Nature 368: 856-859 (1994); Morrison, Nature 368812-13 (1994); Fishwild et al., Nature Biotechnology 14, 845-51 (1996);Neuberger, Nature Biotechnology 14: 826 (1996); and Lonberg and Huszar,Intern. Rev. Immunol. 13, 65-93 (1995).

In case the target antigen (the protein which is detected by theantibody) is presented within the cell, the antibody of the inventioncan be expressed within the cell intracellular antibodies (also known as“intrabodies”) or a particular compartment thereof. Intrabodies areessentially SCA to which intracellular localization signals have beenadded (e.g., ER, mitochondrial, nuclear, cytoplasmic). This technologyhas been successfully applied in the art (for review, see Richardson andMarasco, 1995, TIBTECH vol. 13). Intrabodies have been shown tovirtually eliminate the expression of otherwise abundant cell surfacereceptors and to inhibit a protein function within a cell (See, forexample, Richardson et al., 1995, Proc. Natl. Acad. Sci. USA 92:3137-3141; Deshane et al., 1994, Gene Ther. 1: 332-337; Marasco et al.,1998 Human Gene Ther 9: 1627-42; Shaheen et al., 1996 J. Virol. 70:3392-400; Werge, T. M. et al., 1990, FEBS Letters 274:193-198; Carlson,J. R. 1993 Proc. Natl. Acad. Sci. USA 90:7427-7428; Biocca, S. et al.,1994, Bio/Technology 12: 396-399; Chen, S-Y. et al., 1994, Human GeneTherapy 5:595-601; Duan, L et al., 1994, Proc. Natl. Acad. Sci. USA91:5075-5079; Chen, S-Y. et al., 1994, Proc. Natl. Acad. Sci. USA91:5932-5936; Beerli, R. R. et al., 1994, J. Biol. Chem.269:23931-23936; Mhashilkar, A. M. et al., 1995, EMBO J. 14:1542-1551;PCT Publication No. WO 94/02610 by Marasco et al.; and PCT PublicationNo. WO 95/03832 by Duan et al.).

To prepare an intracellular antibody expression vector, the cDNAencoding the antibody light and heavy chains specific for the targetprotein of interest are isolated, typically from a hybridoma thatsecretes a monoclonal antibody specific for the marker. Hybridomassecreting anti-marker monoclonal antibodies, or recombinant monoclonalantibodies, can be prepared using methods known in the art. Once amonoclonal antibody specific for the marker protein is identified (e.g.,either a hybridoma-derived monoclonal antibody or a recombinant antibodyfrom a combinatorial library), DNAs encoding the light and heavy chainsof the monoclonal antibody are isolated by standard molecular biologytechniques. For hybridoma derived antibodies, light and heavy chaincDNAs can be obtained, for example, by PCR amplification or cDNA libraryscreening. For recombinant antibodies, such as from a phage displaylibrary, cDNA encoding the light and heavy chains can be recovered fromthe display package (e.g., phage) isolated during the library screeningprocess and the nucleotide sequences of antibody light and heavy chaingenes are determined. For example, many such sequences are disclosed inKabat, E. A., et al. (1991) Sequences of Proteins of ImmunologicalInterest, Fifth Edition, U.S. Department of Health and Human Services,NIH Publication No. 91-3242 and in the “Vbase” human germline sequencedatabase. Once obtained, the antibody light and heavy chain sequencesare cloned into a recombinant expression vector using standard methods.

For cytoplasmic expression of the light and heavy chains, the nucleotidesequences encoding the hydrophobic leaders of the light and heavy chainsare removed. An intracellular antibody expression vector can encode anintracellular antibody in one of several different forms. For example,in one embodiment, the vector encodes full-length antibody light andheavy chains such that a full-length antibody is expressedintracellularly. In another embodiment, the vector encodes a full-lengthlight chain but only the VH/CH1 region of the heavy chain such that aFab fragment is expressed intracellularly. In another embodiment, thevector encodes a single chain antibody (scFv) wherein the variableregions of the light and heavy chains are linked by a flexible peptidelinker [e.g., (Gly₄Ser)₃ and expressed as a single chain molecule. Toinhibit marker activity in a cell, the expression vector encoding theintracellular antibody is introduced into the cell by standardtransfection methods, as discussed hereinbefore.

Once antibodies are obtained, they may be tested for activity, forexample via ELISA.

Downregulation of the polynucleotide-of-interest can be also achieved byRNA silencing. As used herein, the phrase “RNA silencing” refers to agroup of regulatory mechanisms [e.g. RNA interference (RNAi),transcriptional gene silencing (TGS), post-transcriptional genesilencing (PTGS), quelling, co-suppression, and translationalrepression] mediated by RNA molecules which result in the inhibition or“silencing” of the expression of a corresponding protein-coding gene.RNA silencing has been observed in many types of organisms, includingplants, animals, and fungi.

As used herein, the term “RNA silencing agent” refers to an RNA which iscapable of inhibiting or “silencing” the expression of a target gene. Incertain embodiments, the RNA silencing agent is capable of preventingcomplete processing (e.g., the full translation and/or expression) of anmRNA molecule through a post-transcriptional silencing mechanism. RNAsilencing agents include noncoding RNA molecules, for example RNAduplexes comprising paired strands, as well as precursor RNAs from whichsuch small non-coding RNAs can be generated. Exemplary RNA silencingagents include dsRNAs such as siRNAs, miRNAs and shRNAs. In oneembodiment, the RNA silencing agent is capable of inducing RNAinterference. In another embodiment, the RNA silencing agent is capableof mediating translational repression.

The RNA silencing agent can be directed to a specific compartment withinthe cells, such as to the nucleus (see e.g., Shim M S and Kwon Y J.2009, “Controlled cytoplasmic and nuclear localization of plasmid DNAand siRNA by differentially tailored polyethylenimine”; J. ControlRelease. 133:206-13, Epub 2008 Nov. 1), nucleoli, and the like.

RNA interference refers to the process of sequence-specificpost-transcriptional gene silencing in animals mediated by shortinterfering RNAs (siRNAs). The corresponding process in plants iscommonly referred to as post-transcriptional gene silencing or RNAsilencing and is also referred to as quelling in fungi. The process ofpost-transcriptional gene silencing is thought to be anevolutionarily-conserved cellular defense mechanism used to prevent theexpression of foreign genes and is commonly shared by diverse flora andphyla. Such protection from foreign gene expression may have evolved inresponse to the production of double-stranded RNAs (dsRNAs) derived fromviral infection or from the random integration of transposon elementsinto a host genome via a cellular response that specifically destroyshomologous single-stranded RNA or viral genomic RNA.

The presence of long dsRNAs in cells stimulates the activity of aribonuclease III enzyme referred to as dicer. Dicer is involved in theprocessing of the dsRNA into short pieces of dsRNA known as shortinterfering RNAs (siRNAs). Short interfering RNAs derived from diceractivity are typically about 21 to about 23 nucleotides in length andcomprise about 19 base pair duplexes. The RNAi response also features anendonuclease complex, commonly referred to as an RNA-induced silencingcomplex (RISC), which mediates cleavage of single-stranded RNA havingsequence complementary to the antisense strand of the siRNA duplex.Cleavage of the target RNA takes place in the middle of the regioncomplementary to the antisense strand of the siRNA duplex.

Accordingly, the present invention contemplates use of dsRNA todownregulate protein expression from mRNA.

According to one embodiment, the dsRNA is greater than 30 bp. The use oflong dsRNAs (i.e. dsRNA greater than 30 bp) has been very limited owingto the belief that these longer regions of double stranded RNA willresult in the induction of the interferon and PKR response. However, theuse of long dsRNAs can provide numerous advantages in that the cell canselect the optimal silencing sequence alleviating the need to testnumerous siRNAs; long dsRNAs will allow for silencing libraries to haveless complexity than would be necessary for siRNAs; and, perhaps mostimportantly, long dsRNA could prevent viral escape mutations when usedas therapeutics.

Various studies demonstrate that long dsRNAs can be used to silence geneexpression without inducing the stress response or causing significantoff-target effects—see for example [Strat et al., Nucleic AcidsResearch, 2006, Vol. 34, No. 13 3803-3810; Bhargava A et al. Brain Res.Protoc. 2004; 13:115-125; Diallo M., et al., Oligonucleotides. 2003;13:381-392; Paddison P. J., et al., Proc. Natl Acad. Sci. USA. 2002;99:1443-1448; Tran N., et al., FEBS Lett. 2004; 573:127-134].

In particular, the present invention also contemplates introduction oflong dsRNA (over 30 base transcripts) for gene silencing in cells wherethe interferon pathway is not activated (e.g. embryonic cells andoocytes) see for example Billy et al., PNAS 2001, Vol 98, pages14428-14433. and Diallo et al, Oligonucleotides, Oct. 1, 2003, 13(5):381-392. doi:10.1089/154545703322617069.

The present invention also contemplates introduction of long ds-RNAspecifically designed not to induce the interferon and PKR pathways fordownregulating gene expression. For example, Shinagwa and Ishii [Genes &Dev. 17 (11): 1340-1345, 2003] have developed a vector, named pDECAP, toexpress long double-strand RNA from an RNA polymerase II (Pol II)promoter. Because the transcripts from pDECAP lack both the 5′-capstructure and the 3′-poly(A) tail that facilitate ds-RNA export to thecytoplasm, long ds-RNA from pDECAP does not induce the interferonresponse.

Another method of evading the interferon and PKR pathways in mammaliansystems is by introduction of small inhibitory RNAs (siRNAs) either viatransfection or endogenous expression.

The term “siRNA” refers to small inhibitory RNA duplexes (generallybetween 18-30 basepairs) that induce the RNA interference (RNAi)pathway. Typically, siRNAs are chemically synthesized as 21 mers with acentral 19 bp duplex region and symmetric 2-base 3′-overhangs on thetermini, although it has been recently described that chemicallysynthesized RNA duplexes of 25-30 base length can have as much as a100-fold increase in potency compared with 21 mers at the same location.The observed increased potency obtained using longer RNAs in triggeringRNAi is theorized to result from providing Dicer with a substrate (27mer) instead of a product (21 mer) and that this improves the rate orefficiency of entry of the siRNA duplex into RISC.

It has been found that position of the 3′-overhang influences potency ofan siRNA and asymmetric duplexes having a 3′-overhang on the antisensestrand are generally more potent than those with the 3′-overhang on thesense strand (Rose et al., 2005). This can be attributed to asymmetricalstrand loading into RISC, as the opposite efficacy patterns are observedwhen targeting the antisense transcript.

The strands of a double-stranded interfering RNA (e.g., an siRNA) may beconnected to form a hairpin or stem-loop structure (e.g., an shRNA).Thus, as mentioned the RNA silencing agent of the present invention mayalso be a short hairpin RNA (shRNA).

A non-limiting example for an siRNA which can be used to down regulateRRN3 (RNA polymerase I transcription factor homolog) expression level ina cell of a subject is Rrn3 siRNA (h): sc-106866 (Santa CruzBiotechnology, Inc. Santa Cruz, Calif., USA). In addition,downregulation of RRN3 can be achieved by Rrn3 shRNA plasmid (h):sc-106866-SH and Rrn3 shRNA (h) Lentiviral Particles: sc-106866-V((Santa Cruz Biotechnology, Inc. Santa Cruz, Calif., USA).

The term “shRNA”, as used herein, refers to an RNA agent having astem-loop structure, comprising a first and second region ofcomplementary sequence, the degree of complementarity and orientation ofthe regions being sufficient such that base pairing occurs between theregions, the first and second regions being joined by a loop region, theloop resulting from a lack of base pairing between nucleotides (ornucleotide analogs) within the loop region. The number of nucleotides inthe loop is a number between and including 3 to 23, or 5 to 15, or 7 to13, or 4 to 9, or 9 to 11. Some of the nucleotides in the loop can beinvolved in base-pair interactions with other nucleotides in the loop.Examples of oligonucleotide sequences that can be used to form the loopinclude 5′-UUCAAGAGA-3′ (Brummelkamp, T. R. et al. (2002) Science 296:550) and 5′-UUUGUGUAG-3′ (Castanotto, D. et al. (2002) RNA 8:1454). Itwill be recognized by one of skill in the art that the resulting singlechain oligonucleotide forms a stem-loop or hairpin structure comprisinga double-stranded region capable of interacting with the RNAi machinery.

According to another embodiment the RNA silencing agent may be a miRNA.miRNAs are small RNAs made from genes encoding primary transcripts ofvarious sizes. They have been identified in both animals and plants. Theprimary transcript (termed the “pri-miRNA”) is processed through variousnucleolytic steps to a shorter precursor miRNA, or “pre-miRNA.” Thepre-miRNA is present in a folded form so that the final (mature) miRNAis present in a duplex, the two strands being referred to as the miRNA(the strand that will eventually basepair with the target) The pre-miRNAis a substrate for a form of dicer that removes the miRNA duplex fromthe precursor, after which, similarly to siRNAs, the duplex can be takeninto the RISC complex. It has been demonstrated that miRNAs can betransgenically expressed and be effective through expression of aprecursor form, rather than the entire primary form (Parizotto et al.(2004) Genes & Development 18:2237-2242 and Guo et al. (2005) Plant Cell17:1376-1386).

Unlike, siRNAs, miRNAs bind to transcript sequences with only partialcomplementarity (Zeng et al., 2002, Molec. Cell 9:1327-1333) and represstranslation without affecting steady-state RNA levels (Lee et al., 1993,Cell 75:843-854; Wightman et al., 1993, Cell 75:855-862). Both miRNAsand siRNAs are processed by Dicer and associate with components of theRNA-induced silencing complex (Hutvagner et al., 2001, Science293:834-838; Grishok et al., 2001, Cell 106: 23-34; Ketting et al.,2001, Genes Dev. 15:2654-2659; Williams et al., 2002, Proc. Natl. Acad.Sci. USA 99:6889-6894; Hammond et al., 2001, Science 293:1146-1150;Mourlatos et al., 2002, Genes Dev. 16:720-728). A recent report(Hutvagner et al., 2002, Sciencexpress 297:2056-2060) hypothesizes thatgene regulation through the miRNA pathway versus the siRNA pathway isdetermined solely by the degree of complementarity to the targettranscript. It is speculated that siRNAs with only partial identity tothe mRNA target will function in translational repression, similar to anmiRNA, rather than triggering RNA degradation.

Synthesis of RNA silencing agents suitable for use with the presentinvention can be effected as follows. First, the mRNA sequence of thepolynucleotide-of-interest is scanned downstream of the AUG start codonfor AA dinucleotide sequences. Occurrence of each AA and the 3′ adjacent19 nucleotides is recorded as potential siRNA target sites. Preferably,siRNA target sites are selected from the open reading frame, asuntranslated regions (UTRs) are richer in regulatory protein bindingsites. UTR-binding proteins and/or translation initiation complexes mayinterfere with binding of the siRNA endonuclease complex [Tusch1ChemBiochem. 2:239-245]. It will be appreciated though, that siRNAsdirected at untranslated regions may also be effective, as demonstratedfor GAPDH wherein siRNA directed at the 5′ UTR mediated about 90%decrease in cellular GAPDH mRNA and completely abolished protein level(www.ambion.com/techlib/tn/91/912.html).

Second, potential target sites are compared to an appropriate genomicdatabase (e.g., human, mouse, rat etc.) using any sequence alignmentsoftware, such as the BLAST software available from the NCBI server(www.ncbi.nlm nih gov/BLAST/). Putative target sites which exhibitsignificant homology to other coding sequences are filtered out.

Qualifying target sequences are selected as template for siRNAsynthesis. Preferred sequences are those including low G/C content asthese have proven to be more effective in mediating gene silencing ascompared to those with G/C content higher than 55%. Several target sitesare preferably selected along the length of the target gene forevaluation. For better evaluation of the selected siRNAs, a negativecontrol is preferably used in conjunction. Negative control siRNApreferably include the same nucleotide composition as the siRNAs butlack significant homology to the genome. Thus, a scrambled nucleotidesequence of the siRNA is preferably used, provided it does not displayany significant homology to any other gene.

It will be appreciated that the RNA silencing agent of the presentinvention need not be limited to those molecules containing only RNA,but further encompasses chemically-modified nucleotides andnon-nucleotides.

In some embodiments, the RNA silencing agent provided herein can befunctionally associated with a cell-penetrating peptide. As used herein,a “cell-penetrating peptide” is a peptide that comprises a short (about12-30 residues) amino acid sequence or functional motif that confers theenergy-independent (i.e., non-endocytotic) translocation propertiesassociated with transport of the membrane-permeable complex across theplasma and/or nuclear membranes of a cell. The cell-penetrating peptideused in the membrane-permeable complex of the present inventionpreferably comprises at least one non-functional cysteine residue, whichis either free or derivatized to form a disulfide link with adouble-stranded ribonucleic acid that has been modified for suchlinkage. Representative amino acid motifs conferring such properties arelisted in U.S. Pat. No. 6,348,185, the contents of which are expresslyincorporated herein by reference. The cell-penetrating peptides of thepresent invention preferably include, but are not limited to,penetratin, transportan, pIsl, TAT(48-60), pVEC, MTS, and MAP.

mRNAs to be targeted using RNA silencing agents include, but are notlimited to, those whose expression is correlated with an undesiredphenotypic trait. Exemplary mRNAs that may be targeted are those thatencode truncated proteins i.e. comprise deletions. Accordingly the RNAsilencing agent of the present invention may be targeted to a bridgingregion on either side of the deletion. Introduction of such RNAsilencing agents into a cell would cause a down-regulation of themutated protein while leaving the non-mutated protein unaffected.

Another agent capable of downregulating the polynucleotide-of-interestis a DNAzyme molecule capable of specifically cleaving an mRNAtranscript or DNA sequence of the polynucleotide-of-interest. DNAzymesare single-stranded polynucleotides which are capable of cleaving bothsingle and double stranded target sequences (Breaker, R. R. and Joyce,G. Chemistry and Biology 1995; 2:655; Santoro, S. W. & Joyce, G. F.Proc. Natl, Acad. Sci. USA 1997; 943:4262) A general model (the “10-23”model) for the DNAzyme has been proposed. “10-23” DNAzymes have acatalytic domain of 15 deoxyribonucleotides, flanked by twosubstrate-recognition domains of seven to nine deoxyribonucleotideseach. This type of DNAzyme can effectively cleave its substrate RNA atpurine:pyrimidine junctions (Santoro, S. W. & Joyce, G. F. Proc. Natl,Acad. Sci. USA 199; for rev of DNAzymes see Khachigian, L M [Curr OpinMol Ther 4:119-21 (2002)].

Examples of construction and amplification of synthetic, engineeredDNAzymes recognizing single and double-stranded target cleavage siteshave been disclosed in U.S. Pat. No. 6,326,174 to Joyce et al. DNAzymesof similar design directed against the human Urokinase receptor wererecently observed to inhibit Urokinase receptor expression, andsuccessfully inhibit colon cancer cell metastasis in vivo (Itoh et al,20002, Abstract 409, Ann Meeting Am Soc Gen Ther World Wide Web (dot)asgt (dot) org). In another application, DNAzymes complementary tobcr-ab1 oncogenes were successful in inhibiting the oncogenes expressionin leukemia cells, and lessening relapse rates in autologous bone marrowtransplant in cases of CML and ALL.

Downregulation of the polynucleotide-of-interest can also be effected byusing an antisense polynucleotide capable of specifically hybridizingwith an mRNA transcript encoding the polynucleotide-of-interest.

Design of antisense molecules which can be used to efficientlydownregulate the polynucleotide-of-interest must be effected whileconsidering two aspects important to the antisense approach. The firstaspect is delivery of the oligonucleotide into the cytoplasm of theappropriate cells, while the second aspect is design of anoligonucleotide which specifically binds the designated mRNA withincells in a way which inhibits translation thereof.

The prior art teaches of a number of delivery strategies which can beused to efficiently deliver oligonucleotides into a wide variety of celltypes [see, for example, Luft J Mol Med 76: 75-6 (1998); Kronenwett etal. Blood 91: 852-62 (1998); Rajur et al. Bioconjug Chem 8: 935-40(1997); Lavigne et al. Biochem Biophys Res Commun 237: 566-71 (1997) andAoki et al. (1997) Biochem Biophys Res Commun 231: 540-5 (1997)].

In addition, algorithms for identifying those sequences with the highestpredicted binding affinity for their target mRNA based on athermodynamic cycle that accounts for the energetics of structuralalterations in both the target mRNA and the oligonucleotide are alsoavailable [see, for example, Walton et al. Biotechnol Bioeng 65: 1-9(1999)].

Such algorithms have been successfully used to implement an antisenseapproach in cells. For example, the algorithm developed by Walton et al.enabled scientists to successfully design antisense oligonucleotides forrabbit beta-globin (RBG) and mouse tumor necrosis factor-alpha (TNFalpha) transcripts. The same research group has more recently reportedthat the antisense activity of rationally selected oligonucleotidesagainst three model target mRNAs (human lactate dehydrogenase A and Band rat gp130) in cell culture as evaluated by a kinetic PCR techniqueproved effective in almost all cases, including tests against threedifferent targets in two cell types with phosphodiester andphosphorothioate oligonucleotide chemistries.

In addition, several approaches for designing and predicting efficiencyof specific oligonucleotides using an in vitro system were alsopublished (Matveeva et al., Nature Biotechnology 16: 1374-1375 (1998)].

Several clinical trials have demonstrated safety, feasibility andactivity of antisense oligonucleotides. For example, antisenseoligonucleotides suitable for the treatment of cancer have beensuccessfully used [Holmund et al., Curr Opin Mol Ther 1:372-85 (1999)],while treatment of hematological malignancies via antisenseoligonucleotides targeting c-myb gene, p53 and Bcl-2 had enteredclinical trials and had been shown to be tolerated by patients [GerwitzCurr Opin Mol Ther 1:297-306 (1999)].

More recently, antisense-mediated suppression of human heparanase geneexpression has been reported to inhibit pleural dissemination of humancancer cells in a mouse model [Uno et al., Cancer Res 61:7855-60(2001)].

Thus, the current consensus is that recent developments in the field ofantisense technology which, as described above, have led to thegeneration of highly accurate antisense design algorithms and a widevariety of oligonucleotide delivery systems, enable an ordinarilyskilled artisan to design and implement antisense approaches suitablefor downregulating expression of known sequences without having toresort to undue trial and error experimentation.

Another agent capable of downregulating the polynucleotide-of-interestis a ribozyme molecule capable of specifically cleaving an mRNAtranscript encoding the polynucleotide-of-interest. Ribozymes are beingincreasingly used for the sequence-specific inhibition of geneexpression by the cleavage of mRNAs encoding proteins of interest [Welchet al., Curr Opin Biotechnol. 9:486-96 (1998)]. The possibility ofdesigning ribozymes to cleave any specific target RNA has rendered themvaluable tools in both basic research and therapeutic applications. Inthe therapeutics area, ribozymes have been exploited to target viralRNAs in infectious diseases, dominant oncogenes in cancers and specificsomatic mutations in genetic disorders [Welch et al., Clin Diagn Virol.10:163-71 (1998)]. Most notably, several ribozyme gene therapy protocolsfor HIV patients are already in Phase 1 trials. More recently, ribozymeshave been used for transgenic animal research, gene target validationand pathway elucidation. Several ribozymes are in various stages ofclinical trials. ANGIOZYME was the first chemically synthesized ribozymeto be studied in human clinical trials. ANGIOZYME specifically inhibitsformation of the VEGF-r (Vascular Endothelial Growth Factor receptor), akey component in the angiogenesis pathway. Ribozyme Pharmaceuticals,Inc., as well as other firms have demonstrated the importance ofanti-angiogenesis therapeutics in animal models. HEPTAZYME, a ribozymedesigned to selectively destroy Hepatitis C Virus (HCV) RNA, was foundeffective in decreasing Hepatitis C viral RNA in cell culture assays(Ribozyme Pharmaceuticals, Incorporated—WEB home page).

An additional method of regulating the expression of thepolynucleotide-of-interest in cells is via triplex formingoligonuclotides (TFOs). Recent studies have shown that TFOs can bedesigned which can recognize and bind to polypurine/polypirimidineregions in double-stranded helical DNA in a sequence-specific manner.These recognition rules are outlined by Maher III, L. J., et al.,Science, 1989; 245:725-730; Moser, H. E., et al., Science, 1987;238:645-630; Beal, P. A., et al, Science, 1992; 251:1360-1363; Cooney,M., et al., Science, 1988; 241:456-459; and Hogan, M. E., et al., EPPublication 375408. Modification of the oligonuclotides, such as theintroduction of intercalators and backbone substitutions, andoptimization of binding conditions (pH and cation concentration) haveaided in overcoming inherent obstacles to TFO activity such as chargerepulsion and instability, and it was recently shown that syntheticoligonucleotides can be targeted to specific sequences (for a recentreview see Seidman and Glazer, J Clin Invest 2003; 112:487-94).

Another agent capable of downregulating the expression level of thepolynucleotide-of-interest is a small molecule which inhibits theactivity, level and/or interactions of the gene product ofpolynucleotide-of-interest, such as by interfering with the pathway inwhich the gene product of the polynucleotide-of-interest is involved.

Non-limiting examples of small molecules which can be used along withthe method of the invention to treat the subject include Cycloheximideand diterpenoid triepoxide Triptolide (TPT) or a derivative thereof.

For example, when RRN3 is upregulated in the typical RRMS subject thenthe treatment can be with diterpenoid triepoxide Triptolide (TPT) or aderivative thereof; and/or with Cycloheximide or a derivative thereof.

Any of the downregulating agents described hereinabove (e.g., the agentwhich downregulates the gene of the RNA polymerase I pathway, e.g.,siRNA, antibody) can be provided to the subject in need thereof alongwith any of the known multiple sclerosis therapies (e.g., the anti MSdrugs) described hereinabove (combination therapy) and/or withTriptolide or a derivative thereof.

Any of the downregulating agents described above can be administered tothe subject per se, or in a pharmaceutical composition where it is mixedwith suitable carriers or excipients.

As used herein a “pharmaceutical composition” refers to a preparation ofone or more of the active ingredients described herein with otherchemical components such as physiologically suitable carriers andexcipients. The purpose of a pharmaceutical composition is to facilitateadministration of a compound to an organism.

Herein the term “active ingredient” refers to the downregulating agentaccountable for the biological effect.

Hereinafter, the phrases “physiologically acceptable carrier” and“pharmaceutically acceptable carrier” which may be interchangeably usedrefer to a carrier or a diluent that does not cause significantirritation to an organism and does not abrogate the biological activityand properties of the administered compound. An adjuvant is includedunder these phrases.

Herein the term “excipient” refers to an inert substance added to apharmaceutical composition to further facilitate administration of anactive ingredient. Examples, without limitation, of excipients includecalcium carbonate, calcium phosphate, various sugars and types ofstarch, cellulose derivatives, gelatin, vegetable oils and polyethyleneglycols.

Techniques for formulation and administration of drugs may be found in“Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa.,latest edition, which is incorporated herein by reference.

Suitable routes of administration may, for example, include oral,rectal, transmucosal, especially transnasal, intestinal or parenteraldelivery, including intramuscular, subcutaneous and intramedullaryinjections as well as intrathecal, direct intraventricular,intracardiac, e.g., into the right or left ventricular cavity, into thecommon coronary artery, intravenous, intraperitoneal, intranasal, orintraocular injections.

For example, the pharmaceutical composition may be administered using adermal patch which releases the active ingredient [e.g., Diterpenoidtriepoxide Triptolide (TPT) has a molecular weight of 360.40 and it willthus be suitable to be used in a dermal patch].

Conventional approaches for drug delivery to the central nervous system(CNS) include: neurosurgical strategies (e.g., intracerebral injectionor intracerebroventricular infusion); molecular manipulation of theagent (e.g., production of a chimeric fusion protein that comprises atransport peptide that has an affinity for an endothelial cell surfacemolecule in combination with an agent that is itself incapable ofcrossing the BBB) in an attempt to exploit one of the endogenoustransport pathways of the BBB; pharmacological strategies designed toincrease the lipid solubility of an agent (e.g., conjugation ofwater-soluble agents to lipid or cholesterol carriers); and thetransitory disruption of the integrity of the BBB by hyperosmoticdisruption (resulting from the infusion of a mannitol solution into thecarotid artery or the use of a biologically active agent such as anangiotensin peptide). However, each of these strategies has limitations,such as the inherent risks associated with an invasive surgicalprocedure, a size limitation imposed by a limitation inherent in theendogenous transport systems, potentially undesirable biological sideeffects associated with the systemic administration of a chimericmolecule comprised of a carrier motif that could be active outside ofthe CNS, and the possible risk of brain damage within regions of thebrain where the BBB is disrupted, which renders it a suboptimal deliverymethod.

Alternately, one may administer the pharmaceutical composition in alocal rather than systemic manner, for example, via injection of thepharmaceutical composition directly into a tissue region of a patient.

Pharmaceutical compositions of the present invention may be manufacturedby processes well known in the art, e.g., by means of conventionalmixing, dissolving, granulating, dragee-making, levigating, emulsifying,encapsulating, entrapping or lyophilizing processes.

Pharmaceutical compositions for use in accordance with the presentinvention thus may be formulated in conventional manner using one ormore physiologically acceptable carriers comprising excipients andauxiliaries, which facilitate processing of the active ingredients intopreparations which, can be used pharmaceutically. Proper formulation isdependent upon the route of administration chosen.

For injection, the active ingredients of the pharmaceutical compositionmay be formulated in aqueous solutions, preferably in physiologicallycompatible buffers such as Hank's solution, Ringer's solution, orphysiological salt buffer. For transmucosal administration, penetrantsappropriate to the barrier to be permeated are used in the formulation.Such penetrants are generally known in the art.

For oral administration, the pharmaceutical composition can beformulated readily by combining the active compounds withpharmaceutically acceptable carriers well known in the art. Suchcarriers enable the pharmaceutical composition to be formulated astablets, pills, dragees, capsules, liquids, gels, syrups, slurries,suspensions, and the like, for oral ingestion by a patient.Pharmacological preparations for oral use can be made using a solidexcipient, optionally grinding the resulting mixture, and processing themixture of granules, after adding suitable auxiliaries if desired, toobtain tablets or dragee cores. Suitable excipients are, in particular,fillers such as sugars, including lactose, sucrose, mannitol, orsorbitol; cellulose preparations such as, for example, maize starch,wheat starch, rice starch, potato starch, gelatin, gum tragacanth,methyl cellulose, hydroxypropylmethyl-cellulose, sodiumcarbomethylcellulose; and/or physiologically acceptable polymers such aspolyvinylpyrrolidone (PVP). If desired, disintegrating agents may beadded, such as cross-linked polyvinyl pyrrolidone, agar, or alginic acidor a salt thereof such as sodium alginate.

Dragee cores are provided with suitable coatings. For this purpose,concentrated sugar solutions may be used which may optionally containgum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethyleneglycol, titanium dioxide, lacquer solutions and suitable organicsolvents or solvent mixtures. Dyestuffs or pigments may be added to thetablets or dragee coatings for identification or to characterizedifferent combinations of active compound doses.

Pharmaceutical compositions which can be used orally, include push-fitcapsules made of gelatin as well as soft, sealed capsules made ofgelatin and a plasticizer, such as glycerol or sorbitol. The push-fitcapsules may contain the active ingredients in admixture with fillersuch as lactose, binders such as starches, lubricants such as talc ormagnesium stearate and, optionally, stabilizers. In soft capsules, theactive ingredients may be dissolved or suspended in suitable liquids,such as fatty oils, liquid paraffin, or liquid polyethylene glycols. Inaddition, stabilizers may be added. All formulations for oraladministration should be in dosages suitable for the chosen route ofadministration.

For buccal administration, the compositions may take the form of tabletsor lozenges formulated in conventional manner.

For administration by nasal inhalation, the active ingredients for useaccording to the present invention are conveniently delivered in theform of an aerosol spray presentation from a pressurized pack or anebulizer with the use of a suitable propellant, e.g.,dichlorodifluoromethane, trichlorofluoromethane,dichloro-tetrafluoroethane or carbon dioxide. In the case of apressurized aerosol, the dosage unit may be determined by providing avalve to deliver a metered amount. Capsules and cartridges of, e.g.,gelatin for use in a dispenser may be formulated containing a powder mixof the compound and a suitable powder base such as lactose or starch.

The pharmaceutical composition described herein may be formulated forparenteral administration, e.g., by bolus injection or continuousinfusion. Formulations for injection may be presented in unit dosageform, e.g., in ampoules or in multidose containers with optionally, anadded preservative. The compositions may be suspensions, solutions oremulsions in oily or aqueous vehicles, and may contain formulatoryagents such as suspending, stabilizing and/or dispersing agents.

Pharmaceutical compositions for parenteral administration includeaqueous solutions of the active preparation in water-soluble form.Additionally, suspensions of the active ingredients may be prepared asappropriate oily or water based injection suspensions. Suitablelipophilic solvents or vehicles include fatty oils such as sesame oil,or synthetic fatty acids esters such as ethyl oleate, triglycerides orliposomes. Aqueous injection suspensions may contain substances, whichincrease the viscosity of the suspension, such as sodium carboxymethylcellulose, sorbitol or dextran. Optionally, the suspension may alsocontain suitable stabilizers or agents which increase the solubility ofthe active ingredients to allow for the preparation of highlyconcentrated solutions.

Alternatively, the active ingredient may be in powder form forconstitution with a suitable vehicle, e.g., sterile, pyrogen-free waterbased solution, before use.

The pharmaceutical composition of the present invention may also beformulated in rectal compositions such as suppositories or retentionenemas, using, e.g., conventional suppository bases such as cocoa butteror other glycerides.

Pharmaceutical compositions suitable for use in context of the presentinvention include compositions wherein the active ingredients arecontained in an amount effective to achieve the intended purpose. Morespecifically, a therapeutically effective amount means an amount ofactive ingredients (the downregulating agent) effective to prevent,alleviate or ameliorate symptoms of a disorder (e.g., RRMS) or prolongthe survival of the subject being treated.

Determination of a therapeutically effective amount is well within thecapability of those skilled in the art, especially in light of thedetailed disclosure provided herein.

For any preparation used in the methods of the invention, thetherapeutically effective amount or dose can be estimated initially fromin vitro and cell culture assays. For example, a dose can be formulatedin animal models to achieve a desired concentration or titer. Suchinformation can be used to more accurately determine useful doses inhumans.

Toxicity and therapeutic efficacy of the active ingredients describedherein can be determined by standard pharmaceutical procedures in vitro,in cell cultures or experimental animals. The data obtained from thesein vitro and cell culture assays and animal studies can be used informulating a range of dosage for use in human. The dosage may varydepending upon the dosage form employed and the route of administrationutilized. The exact formulation, route of administration and dosage canbe chosen by the individual physician in view of the patient'scondition. (See e.g., Fingl, et al., 1975, in “The Pharmacological Basisof Therapeutics”, Ch. 1 p. 1).

Dosage amount and interval may be adjusted individually to providelevels of the active ingredient are sufficient to induce or suppress thebiological effect (minimal effective concentration, MEC). The MEC willvary for each preparation, but can be estimated from in vitro data.Dosages necessary to achieve the MEC will depend on individualcharacteristics and route of administration. Detection assays can beused to determine plasma concentrations.

Depending on the severity and responsiveness of the condition to betreated, dosing can be of a single or a plurality of administrations,with course of treatment lasting from several days to several weeks oruntil cure is effected or diminution of the disease state is achieved.

The amount of a composition to be administered will, of course, bedependent on the subject being treated, the severity of the affliction,the manner of administration, the judgment of the prescribing physician,etc.

Compositions of the present invention may, if desired, be presented in apack or dispenser device, such as an FDA approved kit, which may containone or more unit dosage forms containing the active ingredient. The packmay, for example, comprise metal or plastic foil, such as a blisterpack. The pack or dispenser device may be accompanied by instructionsfor administration. The pack or dispenser may also be accommodated by anotice associated with the container in a form prescribed by agovernmental agency regulating the manufacture, use or sale ofpharmaceuticals, which notice is reflective of approval by the agency ofthe form of the compositions or human or veterinary administration. Suchnotice, for example, may be of labeling approved by the U.S. Food andDrug Administration for prescription drugs or of an approved productinsert. Compositions comprising a preparation of the inventionformulated in a compatible pharmaceutical carrier may also be prepared,placed in an appropriate container, and labeled for treatment of anindicated condition, as is further detailed above.

According to an aspect of some embodiments of the invention, there isprovided a method of selecting a drug for treating a typical relapsingremitting multiple sclerosis (RRMS) in a subject, the method is effectedby (a) contacting cells of a subject classified as having a typical RRMSwith a plurality of drug molecules, (b) identifying at least one drugmolecule which downregulates a level of expression of at least one geneinvolved in the RNA polymerase I pathway, the at least one drug moleculeis suitable for treating the typical RRMS in the subject, therebyselecting the drug for treating the typical RRMS in the subject.

The plurality of drug molecules can be peptides, RNA, DNA, aptamers andsmall molecules.

According to some embodiments of the invention the polynucleotidesdescribed hereinabove (e.g., oligonucleotides) can form a part of aprobeset.

According to some embodiments of the invention, the probeset comprises aplurality of oligonucleotides and no more than 50 oligonucleotides(e.g., no more than about 40, no more than about 30, e.g., no more thanabout 20, e.g., no more than about 15, e.g., no more than about 10oligonucleotides) wherein an oligonucleotide of the plurality ofoligonucleotides specifically recognizes a polynucleotide of at leastone gene involved in the RNA polymerase pathway. For example, each ofthe oligonucleotides can specifically recognize a polynucleotide of theRNA polymerase I pathway.

According to some embodiments of the invention the probeset comprises aplurality of oligonucleotides and no more than 500 oligonucleotideswherein each of the plurality of oligonucleotides is capable ofspecifically recognizing at least one polynucleotide sequence selectedfrom the group consisting of C22orf8, TLK1, HNRPH1, PLXDC1, TLK1, PKN2,ALS2CR8, FLJ12547, ZNF238, PDPR, NT5E, PASK, HPGD, IL6ST, JARID1A, PASK,LEF1, FLJ10246, MTUS1, FLJ14011, VSIG4, MARCH-VI, FLJ10613, EWSR1,ATP8A1, SLC4A7, FLJ21127, HNRPH1, ABLIM1, ITGA6, ADCY9, CROCC, SH3YL1,SMA4, SPTBN1, DPEP3, PDE3B, AF5Q31, NRCAM, DOCK9, IPW, FLJ20152, SIRPB2,GALNT4, CD28, TXK, ETS1, DGCR5, ZNF192, TCF7, CAMK4, SIM2, MGEA5,TGFBR2, RET, MAPK8IP3, RRN3, DKFZp547H025, FBXW11, ZNF423, DLG1,MGC17330, CD164L1, REPS1, ACHE, ITGB1BP2, LOC94431, LTK, RUNX1, EVER1,KIAA2010, CEACAM7, STX16, SLC4A5, CRTAP, RECQL5, MAGEF1, VIPR1,FLJ10979, TTC3, CRSP2, BAZ2A, GTF2I, MGC50853, KIAA0508, BPHL, LTBP4,FN3KRP, SCARB1, MGC17330, HYAL4, DGKA, FLJ11196, DHRS6, EPHB4,IDI2/GTPBP4, SNTG2, SLC7A6, PMS2L2, KIAA0436, TOSO, THRAP3, T3JAM,LOC283232, LOC92482, PTER, ATM, NUCB2, PIK3R2, MGC1136, CD59, JARID1A,FLJ39616, ABLIM1, PBP, MAPK8IP3, FTS, LHX5, TNFRSF7, MYC, PBXIP1, DATF1,HTF9C, PUS1, KIAA0924, C6orf4, KIAA0372, WDR42A, CRYZL1, TERE1, LTBP4,TTC3, NFATC1, POM121/LOC340318, TOSO, LOC348926/MGC16279/SB153/FLJ10661,SPOCK2, KIAA0515, SLC37A4, CD44, SMARCA2, SPTBN1, C6orf130, TTC3, DLG1,SLC35E2, MCCC1, PMS2L11, RCN3, STX16, FLJ20618, STAT5B, SMARCA2, SATB1,POLR1D, ASXL1, REV1L, PMS2L2/PMS2L5, FLJ12355, CCNB1IP1, FLJ12270,KIAA0692, MCM7, GPSN2, STX16, MMS19L, GTF2I/GTF2IP1, AKAP7, ZNF444,SLC35A3, MGEA5, RUTBC3, C20orf36, RAD17, ALG12, LOC112869, C6orf48,CUTC, LGTN, DEF6, WAC, HNRPH3, NS, KIAA0892, LRPPRC, HMG20A, DDX42,TINP1, ZDHHC17, C19orf2, EIF4B, LOC376745, DKFZP434C171, TH1L, C19orf13,RPL22, PHF15, EWSR1, EIF4B, FAM48A, YT521, NEK9, EIF3S7, RPS6, RPL35A,EEF2, RPL3, RPS6, UBA52, RPL6, RPS6, RPL13, AL353949, AL580863,AF052160, AW128846, AW974481, N92920, BG178274, AW303460, BF057458,AL050035, M59917, AK025422, AI693985, AU158442, AK021460, AL023773,NM_003790, AC005011, M90355, AL353580, U38964, D50683, BE967207, YWHAB,ATP6V1E1, UBB, MRLC2/MRCL3, UQCR, MRLC2, RTN4, UBE2A, RTN4, WDR1, PSMA6,C14orf123, PP1201, TBK1, CAST, CAST, RSN, PSME1, SDF2, GSTO1, CAST,DNCL1, SQRDL, ADIPOR2, ICMT, NDUFA6, NDUFA6, COX17, HIF1AN, FLJ20257,TBPL1, RAPGEF2, CRSP8, APOL1, PAOX, CNDP2, ETFA, DPP3, KPNA1, MGC3036,TUBB2, PDCL, CCL5, CDS2, RAP1GDS1, ATP6V1D, OBRGRP/LEPR, SF4, GCLC,MGST3, BICD2, BRF1, CHST12, EXOSC7, TOR1B, ZFP95, ILK, UNC13A, MTHFD2,CASP10, FLJ45850, CMRF-35H, ARF3, NDOR1, DUSP10, AP1M2, VRK2, GSN, PTRF,RBM19, RABGAP1L, ATP5S, STOM, TFPI2, SLCO3A1, PTPN12, CSF1, SIGLEC6,KIRREL, OBRGRP, TP53AP1, SUHW1, NUP98, IL15RA, MICB, CMRF-35H, SPHK1,TNFRSF6, FLJ11301, LRP5, STOM, EPHA2, SRC, FLJ11301, PSTPIP2, EBP,MCPH1, PTPRF, LIMK2, FSTL4, CBR1, MGC2654, MYCT1, NOL3, MITF, ATP10B,FBXO31, TBX21, LSS, SLC17A3, MNAB, CHPPR, GIF, VAMPS, ABCG2, KIF1B,LOH11CR2A, NID2, RBBP8, ETV7, CTSL, RUFY1, RSU1, PARD3, APOB, ACOX3,DAB2, LDLR, TJP2, GNAS, PARD3, NCKAP1, TAP2, HDGFRP3, LDLR, PIK3R3,HTR2B, GAS2L1, FER1L3, C3orf14, TP53TG3, LEPR, CLIC5, PDE4DIP, ATP9A,ITGB1BP1, INDO, SELP, FHL2, FER1L3, EGF, SIAT8A, HDGFRP3, LRAP, VWF,FLJ10134, IMP-3, DMN, MCTP1, FSTL1, CTNNAL1, RAB27B, THBS1, PROS1,MMRN1, CTTN, AL078596, AI148659, U00956 and M29383.

It will be appreciated that the isolated nucleic acid sequences includedin the kit or the probeset of the present invention can be bound to asolid support e.g., a glass wafer in a specific order, i.e., in the formof a microarray. Alternatively, isolated nucleic acid sequences can besynthesized directly on the solid support using well known prior artapproaches (Seo T S, et al., 2004, Proc. Natl. Acad. Sci. USA, 101:5488-93.). In any case, the isolated nucleic acid sequences are attachedto the support in a location specific manner such that each specificisolated nucleic acid sequence has a specific address on the support(i.e., an addressable location) which denotes the identity (i.e., thesequence) of that specific isolated nucleic acid sequence.

The kit may further include a positive control for an expression levelof at least one of the polynucleotides of the invention (e.g., whichinvolves in the RNA polymerase I pathway). The positive control can beany biological sample derived from a reference subject (i.e., a subjectwith a known course of MS, i.e., BMS or typical RRMS), a biologicalsample with known amount/concentration of the gene product (i.e., RNA orprotein) of at least one of the polynucleotides of the invention; or apre-determined level (amount/concentration) of purified, chemicallysynthesized or recombinantly generated RNA or protein molecules (geneproducts) of the at least one polynucleotide of the invention. The kitmay further comprise instructions for use in classifying a subject asbeing more like to have BMS or typical RRMS, to diagnose BMS or typicalRRMS, to monitor treatment efficiency, to select a treatment regimen, totreat a subject having multiple sclerosis and/or to select for drugssuitable for treating multiple sclerosis.

As used herein the term “about” refers to ±10%.

The terms “comprises”, “comprising”, “includes”, “including”, “having”and their conjugates mean “including but not limited to”.

The term “consisting of means “including and limited to”.

The term “consisting essentially of” means that the composition, methodor structure may include additional ingredients, steps and/or parts, butonly if the additional ingredients, steps and/or parts do not materiallyalter the basic and novel characteristics of the claimed composition,method or structure.

As used herein, the singular form “a”, “an” and “the” include pluralreferences unless the context clearly dictates otherwise. For example,the term “a compound” or “at least one compound” may include a pluralityof compounds, including mixtures thereof.

Throughout this application, various embodiments of this invention maybe presented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theinvention. Accordingly, the description of a range should be consideredto have specifically disclosed all the possible subranges as well asindividual numerical values within that range. For example, descriptionof a range such as from 1 to 6 should be considered to have specificallydisclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numberswithin that range, for example, 1, 2, 3, 4, 5, and 6. This appliesregardless of the breadth of the range.

Whenever a numerical range is indicated herein, it is meant to includeany cited numeral (fractional or integral) within the indicated range.The phrases “ranging/ranges between” a first indicate number and asecond indicate number and “ranging/ranges from” a first indicate number“to” a second indicate number are used herein interchangeably and aremeant to include the first and second indicated numbers and all thefractional and integral numerals therebetween.

As used herein the term “method” refers to manners, means, techniquesand procedures for accomplishing a given task including, but not limitedto, those manners, means, techniques and procedures either known to, orreadily developed from known manners, means, techniques and proceduresby practitioners of the chemical, pharmacological, biological,biochemical and medical arts.

It is appreciated that certain features of the invention, which are, forclarity, described in the context of separate embodiments, may also beprovided in combination in a single embodiment. Conversely, variousfeatures of the invention, which are, for brevity, described in thecontext of a single embodiment, may also be provided separately or inany suitable subcombination or as suitable in any other describedembodiment of the invention. Certain features described in the contextof various embodiments are not to be considered essential features ofthose embodiments, unless the embodiment is inoperative without thoseelements.

Various embodiments and aspects of the present invention as delineatedhereinabove and as claimed in the claims section below find experimentalsupport in the following examples.

EXAMPLES

Reference is now made to the following examples, which together with theabove descriptions illustrate some embodiments of the invention in a nonlimiting fashion.

Generally, the nomenclature used herein and the laboratory proceduresutilized in the present invention include molecular, biochemical,microbiological and recombinant DNA techniques. Such techniques arethoroughly explained in the literature. See, for example, “MolecularCloning: A laboratory Manual” Sambrook et al., (1989); “CurrentProtocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed.(1994); Ausubel et al., “Current Protocols in Molecular Biology”, JohnWiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide toMolecular Cloning”, John Wiley & Sons, New York (1988); Watson et al.,“Recombinant DNA”, Scientific American Books, New York; Birren et al.(eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, ColdSpring Harbor Laboratory Press, New York (1998); methodologies as setforth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis,J. E., ed. (1994); “Current Protocols in Immunology” Volumes I-IIIColigan J. E., ed. (1994); Stites et al. (eds), “Basic and ClinicalImmunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994);Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W.H. Freeman and Co., New York (1980); available immunoassays areextensively described in the patent and scientific literature, see, forexample, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578;3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533;3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521;“Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic AcidHybridization” Hames, B. D., and Higgins S. J., eds. (1985);“Transcription and Translation” Hames, B. D., and Higgins S. J., Eds.(1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “ImmobilizedCells and Enzymes” IRL Press, (1986); “A Practical Guide to MolecularCloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317,Academic Press; “PCR Protocols: A Guide To Methods And Applications”,Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategiesfor Protein Purification and Characterization—A Laboratory CourseManual” CSHL Press (1996); all of which are incorporated by reference asif fully set forth herein. Other general references are providedthroughout this document. The procedures therein are believed to be wellknown in the art and are provided for the convenience of the reader. Allthe information contained therein is incorporated herein by reference.

General Materials and Experimental Methods

Subjects—

31 patients (age 44.5±1.5; female to male ratio 24:7) with BMS werecharacterized by mean EDSS 1.95±0.15, disease duration 17.0±1.3 years,annual EDSS rate 0.13±0.01, annual relapse rate 0.23±0.04. 36 patients(age 40.3±1.8; female to male ratio 8:3) with typical RRMS werecharacterized by mean EDSS 3.54±0.23, disease duration 10.9±1.4 years,annual EDSS rate 0.45±0.06, annual relapse rate 0.64±0.09.

RNA Isolation and Microarray Expression Profiling—

Peripheral blood mononuclear cells (PBMC) were separated onficoll-hypaque gradient. Total RNA was isolated using the TRIzol Reagent(Invitrogen, Carlsbad, Calif.), and cDNA was synthesized, labeled andhybridized to HG-U133A-2 array (Affymetrix, Inc, Santa Clara, Calif.)containing 22,215 gene-transcripts, washed and scanned (Hewlett Packard,GeneArray-TM scanner G2500A) according to manufacturer's protocolAffymetrix (Inc, Santa Clara, Calif.).

Data Analysis—

Data analysis was performed using the Partek Genomics Solution software[World Wide Web (dot) partek (dot) com]. Expression values were computedfrom raw CEL (cell) files by applying the Robust Multi-Chip Average(RMA) background correction algorithm. The RMA correction included: 1)values background correction; 2) quantile normalization; 3) log 2transformation; 4) median polish summarization. In order to avoid thenoise caused by variable set effects each set was normalized topre-saved distribution pattern of a well balanced set used as areference distribution. To reduce batch effect ANOVA multiple modelanalysis was applied. Source of variation was analyzed; nuisance batcheseffects such as working batch, patient age, gender and treatment wereeliminated. Most informative genes (MIGs) were defined as genes withp<0.01 by ANOVA linear contrasts model. For samples classification,principal component analyses (PCA) were performed.

Gene functional annotation, enrichment and pathway analysis wereperformed using functional classification tools, David BioinformaticsResources [Hypertext Transfer Protocol://david (dot) abcc (dot) ncifcrf(dot) gov/home (dot) jsp], and Ingenuity Pathways Analysis web-software[World Wide Web (dot) ingenuity (dot) com]. Enrichment was defined assignificantly (p<0.05) higher proportion of genes in a given gene setthan expected by chance analysis. The study design is demonstrated inFIG. 1.

Example 1

Experimental Results

Identification of Differentiating Genes Between Patients with BMS andPatients with Typical RRMS—

BMS patients differentiated from typical RRMS by 406 MIGs (mostinformative genes), 171 genes were over-expressed (upregulated) and 235were down-expressed (downregulated), with the log fold change rangedfrom −3.1 to 3.3 (FIG. 2).

Table 1 hereinbelow provides the differentiating genes between BMS andtypical RRMS patients.

TABLE 1 Genes which are differentially expressed in blood samples ofbenign multiple sclerosis (BMS) and typical relapsing-remitting multiplesclerosis (RRMS) subjects Log Fold p-value Change SEQ SEQ BMS vs. (BMSvs. Affymetrix ID Representative ID typical typical Probeset ID NO:Public ID NO: RRMS RRMS) Gene Symbol Gene Title 216683_at 1 AL353949 4076.85E−04 −1.129 — — 219629_at 2 NM_017911 408 5.51E−03 −1.117 C22orf8chromosome 22 open reading frame 8 210379_s_at 3 AI469203 409 7.42E−03−1.083 TLK1 tousled-like kinase 1 213472_at 4 AI022387 410 4.25E−03−1.081 HNRPH1 heterogeneous nuclear ribonucleoprotein H1 (H) 219700_at 5NM_020405 411 5.56E−05 −1.081 PLXDC1 plexin domain containing 1211077_s_at 6 Z25421 412 9.89E−04 −1.080 TLK1 tousled-like kinase 1 ///tousled-like kinase 1 210969_at 7 AF118089 413 4.20E−04 −1.078 PKN2protein kinase N2 216298_at 8 AL580863 414 3.57E−03 −1.075 — Similar toT-cell receptor gamma chain V region PT- gamma-1/2 precursor /// Simil219834_at 9 NM_024744 415 1.20E−03 −1.069 ALS2CR8 amyotrophic lateralsclerosis 2 (juvenile) chromosome region, candidate 8 215262_at 10AF052160 416 2.29E−04 −1.068 — Clone 24629 mRNA sequence 220715_at 11NM_024992 417 1.53E−04 −1.067 FLJ12547 hypothetical protein FLJ12547207164_s_at 12 NM_006352 418 4.17E−03 −1.067 ZNF238 zinc finger protein238 220236_at 13 NM_017990 419 7.14E−04 −1.067 PDPR pyruvatedehydrogenase phosphatase regulatory subunit 203939_at 14 NM_002526 4201.84E−03 −1.065 NT5E 5′-nucleotidase, ecto (CD73) 216945_x_at 15 U79240421 2.45E−03 −1.063 PASK PAS domain containing serine/threonine kinase203913_s_at 16 NM_000860 422 4.09E−03 −1.062 HPGD hydroxyprostaglandindehydrogenase 15- (NAD) 204864_s_at 17 BE856546 423 9.98E−03 −1.060IL6ST interleukin 6 signal transducer (gp130, oncostatin M receptor)215698_at 18 AF007135 424 3.73E−03 −1.057 JARID1A Jumonji, AT richinteractive domain 1A (RBBP2-like) 213534_s_at 19 D50925 425 3.86E−03−1.056 PASK PAS domain containing serine/threonine kinase 210948_s_at 20AF294627 426 1.98E−03 −1.056 LEF1 lymphoid enhancer- binding factor 1220458_at 21 NM_018038 427 8.30E−03 −1.055 FLJ10246 hypothetical proteinFLJ10246 212093_s_at 22 AI695017 428 8.37E−03 −1.052 MTUS1 mitochondrialtumor suppressor 1 207120_at 23 NM_022103 429 1.75E−03 −1.050 FLJ14011hypothetical zinc finger protein FLJ14011 204787_at 24 NM_007268 4303.61E−03 −1.050 VSIG4 V-set and immunoglobulin domain containing 4215512_at 25 AK000970 431 1.74E−03 −1.049 MARCH-VI membrane- associatedRING- CH protein VI 46947_at 26 T87245 432 1.23E−03 −1.049 FLJ10613Hypothetical protein FLJ10613 210012_s_at 27 BC000527 433 7.10E−03−1.048 EWSR1 Ewing sarcoma breakpoint region 1 210192_at 28 AB013452 4347.32E−03 −1.048 ATP8A1 ATPase, aminophospholipid transporter (APLT),Class I, type 8A, member 1 207603_at 29 NM_003615 435 2.30E−03 −1.047SLC4A7 solute carrier family 4, sodium bicarbonate cotransporter, member7 218584_at 30 NM_024549 436 7.79E−03 −1.047 FLJ21127 hypotheticalprotein FLJ21127 213470_s_at 31 BF983406 437 8.91E−03 −1.047 HNRPH1heterogeneous nuclear ribonucleoprotein H1 (H) 210461_s_at 32 BC002448438 1.63E−03 −1.047 ABLIM1 actin binding LIM protein 1 217656_at 33AW128846 439 5.27E−04 −1.045 — — 215177_s_at 34 AV733308 440 4.01E−04−1.045 ITGA6 integrin, alpha 6 204498_s_at 35 NM_001116 441 3.72E−04−1.043 ADCY9 adenylate cyclase 9 216419_at 36 AK026910 442 7.82E−03−1.043 CROCC ciliary rootlet coiled-coil, rootletin 204019_s_at 37NM_015677 443 1.11E−03 −1.043 SH3YL1 SH3 domain containing, Ysc84- like1 (S. cerevisiae) 214850_at 38 X75940 444 4.48E−03 −1.043 SMA4 SMA4200672_x_at 39 NM_003128 445 1.59E−03 −1.043 SPTBN1 spectrin, beta, non-erythrocytic 1 220179_at 40 NM_022357 446 1.40E−03 −1.042 DPEP3dipeptidase 3 208591_s_at 41 NM_000922 447 6.54E−05 −1.042 PDE3Bphosphodiesterase 3B, cGMP-inhibited 219199_at 42 NM_014423 448 5.72E−03−1.042 AF5Q31 ALL1 fused gene from 5q31 216959_x_at 43 U55258 4491.65E−03 −1.041 NRCAM neuronal cell adhesion molecule 215041_s_at 44BE259050 450 6.36E−03 −1.040 DOCK9 dedicator of cytokinesis 9 213447_at45 AI672541 451 5.32E−05 −1.040 IPW imprinted in Prader- Willi syndrome218532_s_at 46 NM_019000 452 4.80E−03 −1.040 FLJ20152 hypotheticalprotein FLJ20152 220485_s_at 47 NM_018556 453 1.56E−03 −1.039 SIRPB2signal-regulatory protein beta 2 220442_at 48 NM_003774 454 8.94E−03−1.039 GALNT4 UDP-N-acetyl- alpha-D- galactosamine: polypeptide N-acetylgalactosaminyltransferase 211856_x_at 49 AF222341 455 9.84E−03−1.039 CD28 CD28 antigen (Tp44) 206828_at 50 NM_003328 456 1.62E−03−1.039 TXK TXK tyrosine kinase 214447_at 51 NM_005238 457 3.28E−03−1.038 ETS1 v-ets erythroblastosis virus E26 oncogene homolog 1 (avian)215244_at 52 AI479306 458 6.97E−03 −1.038 DGCR5 DiGeorge syndromecritical region gene 5 (non-coding) 206579_at 53 NM_006298 459 5.64E−03−1.038 ZNF192 zinc finger protein 192 205254_x_at 54 AW027359 4603.05E−03 −1.038 TCF7 transcription factor 7 (T-cell specific, HMG-box)210349_at 55 L24959 461 3.07E−03 −1.037 CAMK4 calcium/calmodulin-dependent protein kinase IV 208157_at 56 NM_009586 462 9.47E−03 −1.037SIM2 single-minded homolog 2 (Drosophila) 214972_at 57 AU144791 4634.25E−03 −1.037 MGEA5 Meningioma expressed antigen 5 (hyaluronidase)207334_s_at 58 NM_003242 464 2.70E−03 −1.037 TGFBR2 transforming growthfactor, beta receptor II (70/80 kDa) 217666_at 59 AW974481 465 1.06E−03−1.037 — — 215771_x_at 60 X15786 466 1.14E−03 −1.036 RET retproto-oncogene (multiple endocrine neoplasia and medullary thyroidcarcinoma 216139_s_at 61 AL031718 467 7.40E−03 −1.036 MAPK8IP3mitogen-activated protein kinase 8 interacting protein 3 216902_s_at 62AF001549 468 4.86E−05 −1.036 RRN3 RRN3 RNA polymerase I transcriptionfactor homolog (yeast) 208265_at 63 NM_020161 469 6.06E−04 −1.036DKFZp547H025 hypothetical protein DKFZp547H025 209456_s_at 64 AB033281470 3.49E−03 −1.036 FBXW11 F-box and WD-40 domain protein 11 217237_at65 Y10615 471 7.72E−03 −1.035 ZNF423 Zinc finger protein 423 217208_s_at66 AL121981 472 2.91E−03 −1.035 DLG1 discs, large homolog 1 (Drosophila)221757_at 67 BE042976 473 1.83E−04 −1.035 MGC17330 HGFL gene /// HGFLgene 213481_at 68 N92920 474 4.47E−03 −1.035 — — 219025_at 69 NM_020404475 2.84E−03 −1.035 CD164L1 CD164 sialomucin- like 1 215201_at 70AW166925 476 9.15E−03 −1.034 REPS1 RALBP1 associated Eps domaincontaining 1 205378_s_at 71 NM_015831 477 6.79E−03 −1.034 ACHEacetylcholinesterase (YT blood group) 219829_at 72 NM_012278 4786.24E−03 −1.033 ITGB1BP2 integrin beta 1 binding protein (melusin) 2216908_x_at 73 AF001549 468 6.22E−04 −1.033 LOC94431 similar to RNApolymerase I transcription factor RRN3 217184_s_at 74 X52213 4794.40E−03 −1.033 LTK leukocyte tyrosine kinase 211181_x_at 75 AF312386480 4.63E−03 −1.033 RUNX1 runt-related transcription factor 1 (acutemyeloid leukemia 1; aml1 oncogene) 214958_s_at 76 AK021738 481 1.62E−03−1.033 EVER1 epidermodysplasia verruciformis 1 220369_at 77 NM_017936482 7.90E−03 −1.033 KIAA2010 KIAA2010 211848_s_at 78 AF006623 4838.77E−04 −1.033 CEACAM7 carcinoembryonic antigen-related cell adhesionmolecule 7 221638_s_at 79 AF008937 484 8.81E−03 −1.033 STX16 syntaxin 16221723_s_at 80 AF243499 485 8.08E−03 −1.033 SLC4A5 solute carrier family4, sodium bicarbonate cotransporter, member 5 201380_at 81 NM_006371 4868.45E−04 −1.032 CRTAP cartilage associated protein 34063_at 82 AB006533487 1.03E−03 −1.032 RECQL5 RecQ protein-like 5 214757_at 83 BG178274 4885.20E−03 −1.032 — Hypothetical gene supported by AK024602 218176_at 84NM_022149 489 4.04E−03 −1.032 MAGEF1 melanoma antigen, family F, 1221977_at 85 AW303460 490 7.35E−03 −1.032 — — 214161_at 86 BF057458 4919.56E−03 −1.031 — — 214857_at 87 AL050035 492 6.21E−03 −1.031 — MRNA;cDNA DKFZp566H0124 (from clone DKFZp566H0124) 216230_x_at 88 M59917 4931.74E−03 −1.031 — — 205019_s_at 89 NM_004624 494 3.56E−03 −1.031 VIPR1vasoactive intestinal peptide receptor 1 221707_s_at 90 BC006116 4957.60E−03 −1.031 FLJ10979 hypothetical protein FLJ10979 /// hypotheticalprotein FLJ10979 208664_s_at 91 AU131711 496 1.15E−04 −1.030 TTC3tetratricopeptide repeat domain 3 215167_at 92 BE567032 497 8.69E−03−1.030 CRSP2 cofactor required for Sp1 transcriptional activation,subunit 2, 150 kDa 215437_x_at 93 BE513659 498 4.06E−03 −1.030 BAZ2Abromodomain adjacent to zinc finger domain, 2A 210892_s_at 94 BC004472499 3.77E−03 −1.029 GTF2I general transcription factor II, i 212400_at95 AL043266 500 1.57E−03 −1.029 MGC50853 hypothetical protein MGC50853215137_at 96 H92070 501 5.46E−03 −1.029 KIAA0508 KIAA0508 protein205750_at 97 NM_004332 502 1.95E−03 −1.028 BPHL biphenyl hydrolase- like(serine hydrolase; breast epithelial mucin- associated an 210628_x_at 98AF051344 503 1.93E−03 −1.028 LTBP4 latent transforming growth factorbeta binding protein 4 218210_at 99 NM_024619 504 1.42E−03 −1.028 FN3KRPfructosamine-3- kinase-related protein 216784_at 100 AK025422 5052.68E−03 −1.028 — Transcribed locus, weakly similar to XP_375174.1hypothetical gene supported by 201819_at 101 NM_005505 506 7.48E−03−1.028 SCARB1 scavenger receptor class B, member 1 214312_at 102AI693985 507 2.93E−03 −1.028 — — 215556_at 103 AU158442 508 3.90E−03−1.028 — — 221756_at 104 BE042976 473 2.52E−03 −1.027 MGC17330 HGFL gene/// HGFL gene 216909_at 105 AK021460 509 5.34E−03 −1.027 — — 220249_at106 NM_012269 510 8.17E−03 −1.027 HYAL4 hyaluronoglucosaminidase 4211272_s_at 107 AF064771 511 3.46E−03 −1.027 DGKA diacylglycerol kinase,alpha 80 kDa 218651_s_at 108 NM_018357 512 7.30E−03 −1.027 FLJ11196acheron 218285_s_at 109 NM_020139 513 2.93E−03 −1.027 DHRS6dehydrogenase/reductase (SDR family) member 6 217385_at 110 AL023773 5142.79E−03 −1.027 — — 202894_at 111 NM_004444 515 1.52E−03 −1.026 EPHB4EPH receptor B4 217631_at 112 AI081107 516 6.97E−03 −1.026 IDI2 ///isopentenyl- GTPBP4 diphosphate delta isomerase 2 /// GTP bindingprotein 4 220487_at 113 NM_018968 517 9.34E−03 −1.026 SNTG2 syntrophin,gamma 2 203579_s_at 114 AI660619 518 1.98E−03 −1.026 SLC7A6 solutecarrier family 7 (cationic amino acid transporter, y+ system), member 6215412_x_at 115 AB017007 519 7.10E−04 −1.026 PMS2L2 postmeioticsegregation increased 2-like 2 212217_at 116 AU154782 520 1.32E−03−1.026 KIAA0436 putative prolyl oligopeptidase 221602_s_at 117 AI084226521 3.58E−04 −1.026 TOSO regulator of Fas- induced apoptosis ///regulator of Fas- induced apoptosis 217847_s_at 118 NM_005119 5228.43E−03 −1.025 THRAP3 thyroid hormone receptor associated protein 3215275_at 119 AW963138 523 9.31E−03 −1.025 T3JAM TRAF3-interacting JunN-terminal kinase (JNK)- activating modulator 221951_at 120 AI739035 5242.65E−03 −1.025 LOC283232 hypothetical protein LOC283232 213224_s_at 121AK025724 525 7.84E−05 −1.024 LOC92482 Hypothetical protein LOC92482218967_s_at 122 BF112019 526 5.08E−03 −1.024 PTER phosphotriesteraserelated 208442_s_at 123 NM_000051 527 9.87E−04 −1.024 ATM ataxiatelangiectasia mutated (includes complementation groups A, C and D)203675_at 124 NM_005013 528 5.38E−03 −1.024 NUCB2 nucleobindin 2207105_s_at 125 NM_005027 529 2.15E−03 −1.023 PIK3R2 phosphoinositide-3-kinase, regulatory subunit 2 (p85 beta) 219144_at 126 NM_024025 5303.23E−03 −1.023 MGC1136 hypothetical protein MGC1136 212463_at 127BE379006 531 9.58E−03 −1.023 CD59 CD59 antigen p18-20 (antigenidentified by monoclonal antibodies 16.3A5, EJ16, E 202040_s_at 128NM_005056 532 8.73E−03 −1.023 JARID1A Jumonji, AT rich interactivedomain 1A (RBBP2-like) 64432_at 129 W05463 533 4.53E−03 −1.023 FLJ39616apoptosis related protein PNAS-1 200965_s_at 130 NM_006720 534 2.98E−03−1.022 ABLIM1 actin binding LIM protein 1 205353_s_at 131 NM_002567 5359.67E−03 −1.022 PBP prostatic binding protein 213177_at 132 AB028989 5369.13E−03 −1.022 MAPK8IP3 mitogen-activated protein kinase 8 interactingprotein 3 218373_at 133 NM_022476 537 6.35E−03 −1.022 FTS fused toeshomolog (mouse) 208333_at 134 NM_022363 538 4.11E−03 −1.022 LHX5 LIMhomeobox 5 206150_at 135 NM_001242 539 8.17E−03 −1.022 TNFRSF7 tumornecrosis factor receptor superfamily, member 7 /// tumor necrosis factorr 202431_s_at 136 NM_002467 540 7.39E−03 −1.022 MYC v-mycmyelocytomatosis viral oncogene homolog (avian) 207838_x_at 137NM_020524 541 3.63E−03 −1.021 PBXIP1 pre-B-cell leukemia transcriptionfactor interacting protein 1 218325_s_at 138 NM_022105 542 1.46E−03−1.021 DATF1 death associated transcription factor 1 218475_at 139NM_022727 543 1.53E−03 −1.021 HTF9C HpaII tiny fragments locus 9C218670_at 140 NM_025215 544 1.05E−03 −1.021 PUS1 pseudouridylatesynthase 1 205594_at 141 NM_014897 545 8.79E−03 −1.021 KIAA0924 KIAA0924protein 215411_s_at 142 AL008730 546 7.21E−03 −1.021 C6orf4 chromosome 6open reading frame 4 203048_s_at 143 NM_014639 547 2.14E−03 −1.020KIAA0372 KIAA0372 216885_s_at 144 AK026481 548 4.07E−04 −1.020 WDR42A WDrepeat domain 42A 219767_s_at 145 NM_005111 549 3.79E−03 −1.020 CRYZL1crystallin, zeta (quinone reductase)- like 1 219131_at 146 NM_013319 5503.21E−03 −1.020 TERE1 transitional epithelia response protein213176_s_at 147 AI910869 551 6.21E−03 −1.020 LTBP4 latent transforminggrowth factor beta binding protein 4 208661_s_at 148 D84294 552 4.85E−03−1.020 TTC3 tetratricopeptide repeat domain 3 208196_x_at 149 NM_006162553 9.44E−03 −1.020 NFATC1 nuclear factor of activated T-cells,cytoplasmic, calcineurin- dependent 1 212178_s_at 150 AK022555 5542.95E−03 −1.020 POM121 /// POM121 membrane LOC340318 glycoprotein (rat)/// hypothetical protein LOC340318 221601_s_at 151 AI084226 521 2.54E−03−1.020 TOSO regulator of Fas- induced apoptosis /// regulator of Fas-induced apoptosis 222013_x_at 152 BE348837 555 5.16E−03 −1.019 LOC348926hypothetical protein /// LOC348926 /// MGC16279 hypothetical protein ///SB153 /// MGC16279 /// FLJ10661 hypothetica 202524_s_at 153 AI952009 5565.43E−03 −1.019 SPOCK2 sparc/osteonectin, cwcv and kazal-like domainsproteoglycan (testican) 2 212068_s_at 154 AB011087 557 9.23E−03 −1.019KIAA0515 KIAA0515 202830_s_at 155 NM_001467 558 5.82E−03 −1.019 SLC37A4solute carrier family 37 (glycerol-6- phosphate transporter), member 4209835_x_at 156 BC004372 559 5.79E−03 −1.019 CD44 CD44 antigen (homingfunction and Indian blood group system) 212257_s_at 157 AW131754 5601.51E−03 −1.019 SMARCA2 SWI/SNF related, matrix associated, actindependent regulator of chromatin, subf 212071_s_at 158 BE968833 5612.68E−03 −1.019 SPTBN1 spectrin, beta, non- erythrocytic 1 213322_at 159AL031778 562 8.31E−04 −1.019 C6orf130 chromosome 6 open reading frame130 210645_s_at 160 D83077 563 2.20E−03 −1.019 TTC3 tetratricopeptiderepeat domain 3 202514_at 161 AW139131 564 4.70E−03 −1.018 DLG1DKFZP586B0319 protein 217122_s_at 162 AL031282 565 4.05E−03 −1.018SLC35E2 solute carrier family 35, member E2 218440_at 163 NM_020166 5669.21E−05 −1.018 MCCC1 methylcrotonoyl- Coenzyme A carboxylase 1 (alpha)210707_x_at 164 U38980 567 3.76E−04 −1.018 PMS2L11 postmeioticsegregation increased 2-like 11 61734_at 165 AI797684 568 3.19E−03−1.018 RCN3 reticulocalbin 3, EF- hand calcium binding domain221500_s_at 166 AK026970 569 1.50E−04 −1.018 STX16 syntaxin 16 219422_at167 NM_0003790 570 6.24E−03 −1.018 — — 222244_s_at 168 AK000749 5715.14E−03 −1.018 FLJ20618 hypothetical protein FLJ20618 212550_at 169AI149535 572 1.46E−03 −1.018 STAT5B signal transducer and activator oftranscription 5B 206544_x_at 170 NM_003070 573 5.64E−03 −1.018 SMARCA2SWI/SNF related, matrix associated, actin dependent regulator ofchromatin, subf 216380_x_at 171 AC005011 574 3.97E−03 −1.018 — —203408_s_at 172 NM_002971 575 6.31E−03 −1.018 SATB1 special AT-richsequence binding protein 1 (binds to nuclear matrix/scaffold-ass218258_at 173 NM_015972 576 2.71E−03 −1.017 POLR1D polymerase (RNA) Ipolypeptide D, 16 kDa 212234_at 174 AL034550 577 5.94E−03 −1.017 ASXL1additional sex combs like 1 (Drosophila) 217461_x_at 175 M90355 5787.56E−03 −1.017 — — 218428_s_at 176 NM_016316 579 8.87E−03 −1.017 REV1LREV1-like (yeast) 215667_x_at 177 AI375694 580 1.00E−03 −1.017 PMS2L2/// postmeiotic PMS2L5 segregation increased 2-like 2 /// postmeioticsegregation increased 220465_at 178 NM_024988 581 2.08E−03 −1.017FLJ12355 hypothetical protein FLJ12355 217988_at 179 NM_021178 5829.05E−03 −1.017 CCNB1IP1 cyclin B1 interacting protein 1 221981_s_at 180AA702154 583 3.45E−03 −1.017 FLJ12270 hypothetical protein FLJ12270212201_at 181 AW274877 584 5.96E−03 −1.017 KIAA0692 KIAA0692 protein208795_s_at 182 D55716 585 1.81E−03 −1.017 MCM7 MCM7 minichromosomemaintenance deficient 7 (S. cerevisiae) 208336_s_at 183 NM_004868 5865.33E−03 −1.017 GPSN2 glycoprotein, synaptic 2 221499_s_at 184 AK026970569 8.49E−03 −1.017 STX16 syntaxin 16 202167_s_at 185 NM_022362 5878.82E−03 −1.017 MMS19L MMS19-like (MET18 homolog, S. cerevisiae)201065_s_at 186 NM_001518 588 4.02E−03 −1.017 GTF2I /// generaltranscription GTF2IP1 factor II, i /// general transcription factor II,i, pseud 211172_x_at 187 AF161075 589 2.00E−03 −1.017 AKAP7 A kinase(PRKA) anchor protein 7 218707_at 188 NM_018337 590 7.16E−03 −1.016ZNF444 zinc finger protein 444 206770_s_at 189 NM_012243 591 9.43E−03−1.016 SLC35A3 solute carrier family 35 (UDP-N- acetylglucosamine(UDP-GlcNAc) transporter), mem 200898_s_at 190 AK002091 592 2.97E−03−1.016 MGEA5 meningioma expressed antigen 5 (hyaluronidase) 215519_x_at191 AI081779 593 3.72E−03 −1.016 RUTBC3 RUN and TBC1 domain containing 3212406_s_at 192 AB028973 594 4.48E−03 −1.016 C20orf36 chromosome 20 openreading frame 36 210826_x_at 193 AF098533 595 4.28E−03 −1.015 RAD17RAD17 homolog (S. pombe) 218444_at 194 NM_024105 596 6.99E−03 −1.015ALG12 asparagine-linked glycosylation 12 homolog (yeast, alpha-1,6-mannosyltransferase 221822_at 195 BE544663 597 4.91E−03 −1.015 LOC112869hypothetical protein BC011981 220755_s_at 196 NM_016947 598 7.95E−04−1.015 C6orf48 chromosome 6 open reading frame 48 218970_s_at 197NM_015960 599 9.75E−03 −1.015 CUTC cutC copper transporter homolog (E.coli) 218253_s_at 198 NM_006893 600 5.75E−03 −1.015 LGTN ligatin221293_s_at 199 NM_022047 601 2.42E−03 −1.015 DEF6 differentiallyexpressed in FDCP 6 homolog (mouse) 217742_s_at 200 NM_016628 6025.14E−03 −1.015 WAC WW domain containing adaptor with coiled-coil207127_s_at 201 NM_021644 603 4.06E−03 −1.014 HNRPH3 heterogeneousnuclear ribonucleoprotein H3 (2H9) 217850_at 202 NM_014366 604 5.81E−03−1.014 NS nucleostemin 212505_s_at 203 AL110250 605 8.73E−03 −1.014KIAA0892 KIAA0892 211971_s_at 204 AI653608 606 2.30E−05 −1.014 LRPPRCleucine-rich PPR- motif containing 216387_x_at 205 AL353580 607 5.15E−03−1.014 — — 218152_at 206 NM_018200 608 8.22E−03 −1.014 HMG20Ahigh-mobility group 20A 201788_at 207 NM_007372 609 4.77E−03 −1.014DDX42 DEAD (Asp-Glu- Ala-Asp) box polypeptide 42 201922_at 208 NM_014886610 6.30E−03 −1.014 TINP1 TGF beta-inducible nuclear protein 1 212982_at209 AI621223 611 4.57E−03 −1.014 ZDHHC17 zinc finger, DHHC domaincontaining 17 214173_x_at 210 AW514900 612 2.20E−04 −1.014 C19orf2chromosome 19 open reading frame 2 211937_at 211 NM_001417 613 3.24E−03−1.014 EIF4B eukaryotic translation initiation factor 4B 216843_x_at 212U38964 614 6.22E−03 −1.014 — — 212854_x_at 213 AB051480 615 1.60E−03−1.013 LOC376745 AG1 212886_at 214 AL080169 616 4.76E−03 −1.013DKFZP434C171 DKFZP434C171 protein 220607_x_at 215 NM_016397 617 3.15E−03−1.012 TH1L TH1-like (Drosophila) 212132_at 216 AL117499 618 5.52E−04−1.011 C19orf13 chromosome 19 open reading frame 13 214042_s_at 217AW071997 619 3.11E−03 −1.011 RPL22 ribosomal protein L22 212660_at 218AI735639 620 5.22E−03 −1.011 PHF15 PHD finger protein 15 208944_at 219D50683 621 5.54E−03 −1.011 — — 210011_s_at 220 BC000527 433 9.77E−03−1.010 EWSR1 Ewing sarcoma breakpoint region 1 211938_at 221 BF247371622 8.55E−03 −1.010 EIF4B eukaryotic translation initiation factor 4B220408_x_at 222 NM_017569 623 6.06E−03 −1.010 FAM48A family withsequence similarity 48, member A 212114_at 223 BE967207 624 9.73E−03−1.010 — Similar to microtubule- associated proteins 1A/1B light chain 3212455_at 224 N36997 625 2.91E−03 −1.009 YT521 splicing factor YT521-B212299_at 225 AL117502 626 6.14E−03 −1.009 NEK9 NIMA (never in mitosisgene a)- related kinase 9 200005_at 226 NM_003753 627 4.23E−03 −1.008EIF3S7 eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDa /// eukaryo 200081_s_at 227 BE741754 628 1.02E−03 −1.007 RPS6ribosomal protein S6 /// ribosomal protein S6 213687_s_at 228 BE968801629 8.26E−03 −1.006 RPL35A ribosomal protein L35a 204102_s_at 229NM_001961 630 5.59E−03 −1.006 EEF2 eukaryotic translation elongationfactor 2 211666_x_at 230 L22453 631 6.17E−03 −1.006 RPL3 ribosomalprotein L3 /// ribosomal protein L3 209134_s_at 231 BC000524 6321.77E−03 −1.005 RPS6 ribosomal protein S6 221700_s_at 232 AF348700 6332.98E−04 −1.005 UBA52 ubiquitin A-52 residue ribosomal protein fusionproduct 1 /// ubiquitin A-52 res 200034_s_at 233 NM_000970 634 9.34E−03−1.005 RPL6 ribosomal protein L6 /// ribosomal protein L6 201254_x_at234 NM_001010 635 7.37E−03 −1.004 RPS6 ribosomal protein S6 212734_x_at235 AI186735 636 8.06E−03 −1.003 RPL13 ribosomal protein L13 217718_s_at236 NM_014052 637 6.36E−03 1.005 YWHAB tyrosine 3-monooxygenase/tryptophan 5- monooxygenase activation protein, beta pol208678_at 237 BC004443 638 8.57E−03 1.006 ATP6V1E1 ATPase, H+transporting, lysosomal 31 kDa, V1 subunit E isoform 1 200633_at 238NM_018955 639 2.94E−03 1.006 UBB ubiquitin B /// ubiquitin B 201318_s_at239 NM_006471 640 1.52E−03 1.007 MRLC2 /// myosin regulatory MRCL3 lightchain MRLC2 /// myosin regulatory light chain MRCL3 202090_s_at 240NM_006830 641 3.41E−03 1.008 UQCR ubiquinol- cytochrome c reductase (6.4kD) subunit 221474_at 241 U26162 642 7.75E−03 1.008 MRLC2 myosinregulatory light chain MRLC2 214629_x_at 242 AF320999 643 3.29E−03 1.009RTN4 reticulon 4 200067_x_at 243 AL078596 644 9.11E−03 1.010 — —201899_s_at 244 NM_003336 645 8.17E−03 1.010 UBE2A ubiquitin-conjugating enzyme E2A (RAD6 homolog) 210968_s_at 245 AF333336 6463.86E−03 1.010 RTN4 reticulon 4 200609_s_at 246 NM_017491 647 5.41E−041.010 WDR1 WD repeat domain 1 208805_at 247 BC002979 648 3.97E−03 1.011PSMA6 proteasome (prosome, macropain) subunit, alpha type, 6 218571_s_at248 NM_014169 649 5.41E−03 1.011 C14orf123 chromosome 14 open readingframe 123 217730_at 249 NM_022152 650 5.26E−03 1.013 PP1201 PP1201protein 218520_at 250 NM_013254 651 9.23E−03 1.013 TBK1 TANK-bindingkinase 1 208908_s_at 251 AF327443 652 7.99E−03 1.014 CAST calpastatin207467_x_at 252 NM_001750 653 8.54E−03 1.014 CAST calpastatin 201975_at253 NM_002956 654 5.39E−03 1.015 RSN restin (Reed- Steinberg cell-expressed intermediate filament-associated protein) 200814_at 254NM_006263 655 2.49E−04 1.015 PSME1 proteasome (prosome, macropain)activator subunit 1 (PA28 alpha) 203090_at 255 NM_006923 656 4.45E−031.015 SDF2 stromal cell-derived factor 2 201470_at 256 NM_004832 6572.35E−03 1.015 GSTO1 glutathione S- transferase omega 1 212586_at 257AA195244 658 6.42E−03 1.016 CAST calpastatin 200703_at 258 NM_003746 6595.88E−03 1.016 DNCL1 dynein, cytoplasmic, light polypeptide 1 217995_at259 NM_021199 660 9.02E−03 1.016 SQRDL sulfide quinone reductase-like(yeast) 201346_at 260 NM_024551 661 3.81E−03 1.016 ADIPOR2 adiponectinreceptor 2 201609_x_at 261 AL578502 662 1.36E−03 1.016 ICMTisoprenylcysteine carboxyl methyltransferase 202000_at 262 BC002772 6636.15E−03 1.016 NDUFA6 NADH dehydrogenase (ubiquinone) 1 alphasubcomplex, 6, 14 kDa 202001_s_at 263 BC002772 663 7.78E−03 1.017 NDUFA6NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14 kDa 203880_at264 NM_005694 664 6.24E−03 1.017 COX17 COX17 homolog, cytochrome coxidase assembly protein (yeast) 218525_s_at 265 NM_017902 665 9.42E−031.017 HIF1AN hypoxia-inducible factor 1, alpha subunit inhibitor219798_s_at 266 NM_019606 666 3.38E−03 1.017 FLJ20257 hypotheticalprotein FLJ20257 208398_s_at 267 NM_004865 667 7.76E−03 1.017 TBPL1TBP-like 1 218358_at 268 NM_024324 668 6.57E−03 1.017 — — 203097_s_at269 NM_014247 669 4.66E−03 1.017 RAPGEF2 Rap guanine nucleotide exchangefactor (GEF) 2 221598_s_at 270 BC002878 670 7.63E−03 1.017 CRSP8cofactor required for Sp1 transcriptional activation, subunit 8, 34 kDa209546_s_at 271 AF323540 671 6.71E−03 1.018 APOL1 apolipoprotein L, 150400_at 272 AI743990 672 7.35E−03 1.018 PAOX polyamine oxidase(exo-N4-amino) 217752_s_at 273 NM_018235 673 4.11E−03 1.018 CNDP2 CNDPdipeptidase 2 (metallopeptidase M20 family) 201931_at 274 NM_000126 6746.90E−03 1.018 ETFA electron-transfer- flavoprotein, alpha polypeptide(glutaric aciduria II) 218567_x_at 275 NM_005700 675 1.00E−02 1.019 DPP3dipeptidylpeptidase 3 202056_at 276 AW051311 676 8.93E−03 1.019 KPNA1Karyopherin alpha 1 (importin alpha 5) 218907_s_at 277 NM_023942 6772.62E−03 1.019 MGC3036 hypothetical protein MGC3036 213726_x_at 278AA515698 678 2.22E−03 1.019 TUBB2 tubulin, beta, 2 204448_s_at 279AF031463 679 7.00E−03 1.019 PDCL phosducin-like 1405_i_at 280 M21121 6809.54E−03 1.019 CCL5 chemokine (C-C motif) ligand 5 212864_at 281 Y16521681 9.17E−03 1.019 CDS2 CDP-diacylglycerol synthase (phosphatidatecytidylyltransferase) 2 209444_at 282 BC001851 682 1.27E−04 1.019RAP1GDS1 RAP1, GTP-GDP dissociation stimulator 1 208898_at 283 AF077614683 2.37E−03 1.019 ATP6V1D ATPase, H+ transporting, lysosomal 34 kDa, V1subunit D 202377_at 284 AW026535 684 5.30E−03 1.019 OBRGRP /// leptinreceptor gene- LEPR related protein /// leptin receptor 209547_s_at 285BC001043 685 4.14E−03 1.020 SF4 splicing factor 4 202922_at 286 BF676980686 4.19E−03 1.020 GCLC glutamate-cysteine ligase, catalytic subunit201403_s_at 287 NM_004528 687 3.64E−03 1.020 MGST3 microsomalglutathione S- transferase 3 213154_s_at 288 AI934125 688 2.75E−03 1.020BICD2 bicaudal D homolog 2 (Drosophila) 215676_at 289 N91109 6898.42E−03 1.021 BRF1 BRF1 homolog, subunit of RNA polymerase IIItranscription initiation factor IIIB 218927_s_at 290 BC002918 6908.09E−03 1.021 CHST12 carbohydrate (chondroitin 4) sulfotransferase 12213648_at 291 AW614427 691 6.11E−03 1.021 EXOSC7 Exosome component 7209593_s_at 292 AF317129 692 8.82E−03 1.021 TOR1B torsin family 1,member B (torsin B) 203731_s_at 293 NM_014569 693 1.78E−03 1.022 ZFP95zinc finger protein 95 homolog (mouse) 201234_at 294 NM_004517 6942.90E−03 1.022 ILK integrin-linked kinase 214817_at 295 BE783668 6958.61E−03 1.022 UNC13A unc-13 homolog A (C. elegans) 201761_at 296NM_006636 696 3.83E−03 1.022 MTHFD2 methylene tetrahydrofolatedehydrogenase (NAD+ dependent), methenyltetrahydrofol 205467_at 297NM_001230 697 6.50E−03 1.022 CASP10 caspase 10, apoptosis-relatedcysteine protease 222318_at 298 AI744673 698 9.20E−03 1.022 FLJ45850FLJ45850 protein 209933_s_at 299 AF020314 699 6.24E−03 1.022 CMRF-35Hleukocyte membrane antigen 200734_s_at 300 BG341906 700 4.33E−03 1.023ARF3 ADP-ribosylation factor 3 219899_x_at 301 NM_014434 701 7.97E−031.023 NDOR1 NADPH dependent diflavin oxidoreductase 1 221563_at 302N36770 702 3.41E−03 1.024 DUSP10 dual specificity phosphatase 1065517_at 303 AA910946 703 4.00E−03 1.024 AP1M2 adaptor-related proteincomplex 1, mu 2 subunit 205126_at 304 NM_006296 704 8.89E−03 1.024 VRK2vaccinia related kinase 2 200696_s_at 305 NM_000177 705 8.30E−03 1.024GSN gelsolin (amyloidosis, Finnish type) 208790_s_at 306 AF312393 7064.43E−03 1.025 PTRF polymerase I and transcript release factor205115_s_at 307 NM_016196 707 8.06E−03 1.025 RBM19 RNA binding motifprotein 19 213982_s_at 308 BG107203 708 8.15E−03 1.025 RABGAP1L RABGTPase activating protein 1- like 206992_s_at 309 NM_015684 709 2.03E−031.025 ATP5S ATP synthase, H+ transporting, mitochondrial F0 complex,subunit s (factor B) 201060_x_at 310 AI537887 710 9.12E−04 1.025 STOMstomatin 209278_s_at 311 L27624 711 7.18E−03 1.026 TFPI2 tissue factorpathway inhibitor 2 210542_s_at 312 BC000585 712 4.38E−03 1.026 SLCO3A1solute carrier organic anion transporter family, member 3A1 202006_at313 NM_002835 713 3.01E−03 1.026 PTPN12 protein tyrosine phosphatase,non- receptor type 12 210557_x_at 314 M76453 714 2.04E−03 1.026 CSF1colony stimulating factor 1 (macrophage) 210796_x_at 315 D86359 7152.95E−03 1.027 SIGLEC6 sialic acid binding Ig-like lectin 6 220825_s_at316 NM_018240 716 9.74E−03 1.027 KIRREL kin of IRRE like (Drosophila)202378_s_at 317 NM_017526 717 2.72E−03 1.027 OBRGRP leptin receptorgene- related protein 210241_s_at 318 AB007458 718 3.02E−03 1.027TP53AP1 TP53 activated protein 1 213069_at 319 AI148659 719 2.90E−031.027 — — 216034_at 320 AA558468 720 9.90E−03 1.027 SUHW1 suppressor ofhairy wing homolog 1 (Drosophila) 210793_s_at 321 U41815 721 2.64E−031.029 NUP98 nucleoporin 98 kDa 207375_s_at 322 NM_002189 722 3.71E−031.029 IL15RA interleukin 15 receptor, alpha 206247_at 323 NM_005931 7232.70E−03 1.029 MICB MHC class I polypeptide-related sequence B217078_s_at 324 AJ010102 724 9.65E−03 1.029 CMRF-35H leukocyte membraneantigen 219257_s_at 325 NM_021972 725 1.62E−03 1.030 SPHK1 sphingosinekinase 1 204781_s_at 326 NM_000043 726 8.44E−03 1.030 TNFRSF6 tumornecrosis factor receptor superfamily, member 6 221536_s_at 327 AL136897727 2.28E−03 1.030 FLJ11301 hypothetical protein FLJ11301 209468_at 328AB017498 728 8.91E−03 1.030 LRP5 low density lipoprotein receptor-related protein 5 201061_s_at 329 M81635 729 1.46E−04 1.030 STOMstomatin 203499_at 330 NM_004431 730 6.49E−03 1.031 EPHA2 EPH receptorA2 213324_at 331 AK024281 731 7.63E−03 1.031 SRC v-src sarcoma(Schmidt-Ruppin A- 2) viral oncogene homolog (avian) 221535_at 332AL136897 727 3.81E−03 1.031 FLJ11301 hypothetical protein FLJ11301219938_s_at 333 NM_024430 732 3.19E−03 1.032 PSTPIP2 proline-serine-threonine phosphatase interacting protein 2 213787_s_at 334 AV702405 7331.78E−03 1.032 EBP emopamil binding protein (sterol isomerase) 219592_at335 NM_024596 734 8.43E−03 1.032 MCPH1 microcephaly, primary autosomalrecessive 1 200637_s_at 336 AI762627 735 5.52E−03 1.033 PTPRF proteintyrosine phosphatase, receptor type, F 202193_at 337 NM_005569 7364.88E−03 1.033 LIMK2 LIM domain kinase 2 214859_at 338 AI635302 7378.68E−03 1.034 FSTL4 follistatin-like 4 209213_at 339 BC002511 7385.69E−03 1.034 CBR1 carbonyl reductase 1 218945_at 340 NM_024109 7393.75E−03 1.034 MGC2654 hypothetical protein MGC2654 220471_s_at 341NM_025107 740 8.29E−03 1.035 MYCT1 myc target 1 59625_at 342 AI912351741 5.19E−03 1.035 NOL3 nucleolar protein 3 (apoptosis repressor withCARD domain) 207233_s_at 343 NM_000248 742 2.93E−03 1.035 MITFmicrophthalmia- associated transcription factor 214070_s_at 344 AW006935743 5.14E−03 1.036 ATP10B ATPase, Class V, type 10B 219785_s_at 345NM_024735 744 5.84E−03 1.036 FBXO31 F-box protein 31 220684_at 346NM_013351 745 3.34E−03 1.037 TBX21 T-box 21 202245_at 347 AW084510 7467.02E−03 1.037 LSS lanosterol synthase (2,3-oxidosqualene- lanosterolcyclase) 207298_at 348 NM_006632 747 6.68E−03 1.037 SLC17A3 solutecarrier family 17 (sodium phosphate), member 3 220201_at 349 NM_018835748 3.85E−03 1.038 MNAB membrane associated DNA binding protein203208_s_at 350 BF214329 749 6.89E−04 1.038 CHPPR likely ortholog ofchicken chondrocyte protein with a poly- proline region 207033_at 351NM_005142 750 3.42E−04 1.039 GIF gastric intrinsic factor (vitamin Bsynthesis) 204929_s_at 352 NM_006634 751 6.38E−03 1.039 VAMP5vesicle-associated membrane protein 5 (myobrevin) 209735_at 353 AF098951752 7.05E−03 1.039 ABCG2 ATP-binding cassette, sub-family G (WHITE),member 2 209234_at 354 BF939474 753 3.31E−04 1.039 KIF1B kinesin familymember 1B 210102_at 355 BC001234 754 5.97E−03 1.040 LOH11CR2A loss ofheterozygosity, 11, chromosomal region 2, gene A 204114_at 356 NM_007361755 4.45E−03 1.041 NID2 nidogen 2 (osteonidogen) 203344_s_at 357NM_002894 756 1.33E−03 1.041 RBBP8 retinoblastoma binding protein 8216891_at 358 U00956 757 5.03E−03 1.042 — — 221680_s_at 359 AF147782 7589.08E−03 1.042 ETV7 ets variant gene 7 (TEL2 oncogene) 202087_s_at 360NM_001912 759 3.63E−03 1.042 CTSL cathepsin L 218243_at 361 NM_025158760 6.62E−03 1.043 RUFY1 RUN and FYVE domain containing 1 201980_s_at362 NM_012425 761 5.59E−03 1.044 RSU1 Ras suppressor protein 1221280_s_at 363 NM_019619 762 4.65E−04 1.044 PARD3 par-3 partitioningdefective 3 homolog (C. elegans) 205108_s_at 364 NM_000384 763 2.36E−041.045 APOB apolipoprotein B (including Ag(x) antigen) 204241_at 365BF055171 764 6.95E−04 1.045 ACOX3 acyl-Coenzyme A oxidase 3, pristanoyl201278_at 366 N21202 765 2.71E−03 1.049 DAB2 Disabled homolog 2,mitogen- responsive phosphoprotein (Drosophila) 202067_s_at 367 AI861942766 1.95E−03 1.050 LDLR low density lipoprotein receptor (familialhypercholesterolemia) 202085_at 368 NM_004817 767 3.10E−03 1.051 TJP2tight junction protein 2 (zona occludens 2) 214157_at 369 AA401492 7684.90E−03 1.053 GNAS GNAS complex locus 221526_x_at 370 AF196185 7692.72E−03 1.053 PARD3 par-3 partitioning defective 3 homolog (C. elegans)207738_s_at 371 NM_013436 770 2.00E−03 1.054 NCKAP1 NCK-associatedprotein 1 204769_s_at 372 NM_000544 771 3.15E−03 1.054 TAP2 transporter2, ATP- binding cassette, sub-family B (MDR/TAP) 216693_x_at 373AL133102 772 6.34E−03 1.055 HDGFRP3 hepatoma-derived growth factor,related protein 3 202068_s_at 374 NM_000527 773 5.72E−03 1.057 LDLR lowdensity lipoprotein receptor (familial hypercholesterolemia) 202743_at375 BE622627 774 7.96E−04 1.061 PIK3R3 phosphoinositide-3- kinase,regulatory subunit 3 (p55, gamma) 206638_at 376 NM_000867 775 7.47E−031.061 HTR2B 5- hydroxytryptamine (serotonin) receptor 2B 31874_at 377Y07846 776 2.32E−03 1.061 GAS2L1 growth arrest- specific 2 like 1201798_s_at 378 NM_013451 777 5.01E−03 1.062 FER1L3 fer-1-like 3,myoferlin (C. elegans) 219288_at 379 NM_020685 778 6.67E−04 1.063C3orf14 chromosome 3 open reading frame 14 220167_s_at 380 NM_015369 7795.44E−04 1.064 TP53TG3 TP53TG3 protein 211354_s_at 381 U52913 7801.67E−03 1.066 LEPR leptin receptor 213317_at 382 AL049313 781 7.15E−031.067 CLIC5 Chloride intracellular channel 5 212390_at 383 AB007923 7828.15E−03 1.070 PDE4DIP phosphodiesterase 4D interacting protein(myomegalin) 212062_at 384 AB014511 783 8.65E−03 1.070 ATP9A ATPase,Class II, type 9A 203337_x_at 385 NM_004763 784 6.03E−03 1.071 ITGB1BP1integrin beta 1 binding protein 1 210029_at 386 M34455 785 5.97E−031.073 INDO indoleamine-pyrrole 2,3 dioxygenase 206049_at 387 NM_003005786 8.60E−03 1.074 SELP selectin P (granule membrane protein 140 kDa,antigen CD62) 202949_s_at 388 NM_001450 787 6.99E−03 1.076 FHL2 four anda half LIM domains 2 211864_s_at 389 AF207990 788 7.27E−03 1.076 FER1L3fer-1-like 3, myoferlin (C. elegans) 206254_at 390 NM_001963 7895.83E−03 1.077 EGF epidermal growth factor (beta- urogastrone) 210073_at391 L32867 790 5.66E−04 1.077 SIAT8A sialyltransferase 8A (alpha-N-acetylneuraminate: alpha-2,8- sialyltransferase, GD 209524_at 392AK001280 791 1.03E−03 1.080 HDGFRP3 hepatoma-derived growth factor,related protein 3 219759_at 393 NM_022350 792 8.03E−04 1.081 LRAPleukocyte-derived arginine aminopeptidase 202112_at 394 NM_000552 7931.22E−03 1.082 VWF von Willebrand factor 219410_at 395 NM_018004 7944.81E−03 1.083 FLJ10134 hypothetical protein FLJ10134 203819_s_at 396AU160004 795 3.58E−03 1.088 IMP-3 IGF-II mRNA- binding protein 3212730_at 397 AK026420 796 3.19E−03 1.090 DMN desmuslin 220122_at 398NM_024717 797 5.82E−03 1.090 MCTP1 multiple C2- domains with twotransmembrane regions 1 208782_at 399 BC000055 798 2.14E−03 1.095 FSTL1follistatin-like 1 202468_s_at 400 NM_003798 799 1.36E−03 1.096 CTNNAL1catenin (cadherin- associated protein), alpha-like 1 207018_s_at 401NM_004163 800 4.02E−03 1.101 RAB27B RAB27B, member RAS oncogene family210354_at 402 M29383 801 4.60E−03 1.102 — — 201110_s_at 403 NM_003246802 9.38E−03 1.111 THBS1 thrombospondin 1 207808_s_at 404 NM_000313 8032.92E−03 1.114 PROS1 protein S (alpha) 205612_at 405 NM_007351 8047.97E−03 1.118 MMRN1 multimerin 1 214073_at 406 BG475299 805 2.37E−031.121 CTTN cortactin Presented are the 406 differentiating genes givenby the gene name and description, the Affymetrix probeset identificationnumber, and a representative GenBank Accession number between BMS andtypical RRMS patients. p-value - statistical significance by ANOVA; LogFold Change = refers to the logarithms fold change between theexpression level of a polynucleotide in a blood sample of a BMS subjectas compared to the expression level in a blood sample of a typical RRMSsubject: The (−) sign means that the polynucleotide is downregulated(decreased in level) in BMS as compared to typical RRMS subjects; andthe (+) sign means that the polynucleotide is upregulated (increased inlevel) in BMS as compared to typical RRMS subjects.

Table 2 hereinbelow discloses additional polynucleotides (RNAalternative transcripts) of the above identified 406 genes whichexpression level is differentiating between typical RRMS and BMS.

TABLE 2 SEQ PROBESET ID NO: Refseq Ids/SEQ ID NO: REFSEQ_UNIGENEREFSEQ_BAND 216683_at 1 —/ — — 219629_at 2 NM_017911/ C22ORF8 Hs.265018997 210379_s_at 3 NM_012290/ TLK1 Hs.470586 948 213472_at 4 —/ — —219700_at 5 NM_020405/ PLXDC1 Hs.125036 1022 211077_s_at 6 NM_012290/TLK1 Hs.470586 948 210969_at 7 —/ — — 216298_at 8 —/ — — 219834_at 9NM_024744/ ALS2CR8 Hs.444982 1051 215262_at 10 —/ — — 220715_at 11 —/ —— 207164_s_at 12 NM_205768/ NM_006352/ ZNF238, Hs.69997, 1103 1133ZNF238, Hs.69997, 220236_at 13 NM_017990/ PDPR Hs.461183 999 203939_at14 NM_002526/ NT5E Hs.153952 865 216945_x_at 15 NM_015148/ PASKHs.397891 970 203913_s_at 16 NM_000860/ HPGD Hs.77348 834 204864_s_at 17NM_175767/ NM_002183/ IL6ST, Hs.532082, 1088 1189 IL6ST, Hs.532082,215698_at 18 —/ — — 213534_s_at 19 NM_015148/ PASK Hs.397891 970210948_s_at 20 NM_016269/ LEF1 Hs.125132 988 220458_at 21 NM_018038/FLJ10246 Hs.274274 1001 212093_s_at 22 NM_020749/ NM_001001931/NM_001001925/ NM_001001924/ NM_001001927/ MTUS1, Hs.7946, 1025 1114 11821216 1234 MTUS1, Hs.7946, MTUS1, Hs.7946, MTUS1, Hs.7946, MTUS1,Hs.7946, 207120_at 23 NM_022103/ FLJ14011 Hs.433473 1033 204787_at 24NM_007268/ VSIG4 Hs.8904 939 215512_at 25 —/ — — 46947_at 26 —/ — —210012_s_at 27 —/ — — 210192_at 28 NM_006095/ ATP8A1 Hs.435052 918207603_at 29 —/ — — 218584_at 30 NM_024549/ FLJ21127 Hs.211511 1047213470_s_at 31 NM_005520/ HNRPH1 Hs.202166 912 210461_s_at 32 NM_006720/NM_002313/ NM_001003407/ NM_001003408/ ABLIM1, Hs.438236, 930 1120 11871232 ABLIM1, Hs.438236, ABLIM1, Hs.438236, ABLIM1, Hs.438236, 217656_at33 —/ — — 215177_s_at 34 NM_000210/ ITGA6 Hs.133397 826 204498_s_at 35NM_001116/ ADCY9 Hs.391860 848 216419_at 36 —/ — — 204019_s_at 37NM_015677/ SH3YL1 Hs.515951 979 214850_at 38 NM_207331/ LOC153561Hs.545578 1106 200672_x_at 39 NM_003128/ SPTBN1 Hs.503178 872 220179_at40 NM_022357/ DPEP3 Hs.302028 1037 208591_s_at 41 NM_000922/ PDE3BHs.445711 835 219199_at 42 NM_014423/ AF5Q31 Hs.519313 958 216959_x_at43 NM_005010/ NRCAM Hs.21422 899 215041_s_at 44 NM_015296/ DOCK9Hs.314413 973 213447_at 45 —/ — — 218532_s_at 46 NM_019000/ FLJ20152Hs.481704 1016 220485_s_at 47 NM_018556/ NM_080816/ SIRPB2, Hs.50716,1011 1150 SIRPB2, Hs.50716, 220442_at 48 NM_003774/ GALNT4 Hs.534374 881211856_x_at 49 NM_006139/ CD28 Hs.1987 919 206828_at 50 NM_003328/ TXKHs.479669 875 214447_at 51 NM_005238/ ETS1 Hs.369438 907 215244_at 52 —/— — 206579_at 53 NM_006298/ ZNF192 Hs.57679 922 205254_x_at 54NM_201632/ NM_201634/ NM_213648/ NM_003202/ TCF7, Hs.519580, 1099 11731215 1219 TCF7, Hs.519580, TCF7, Hs.519580, TCF7, Hs.519580, 210349_at55 NM_001744/ CAMK4 Hs.220629 856 208157_at 56 NM_009586/ SIM2 Hs.146186942 214972_at 57 —/ — — 207334_s_at 58 NM_003242/ TGFBR2 Hs.82028 873217666_at 59 —/ — — 215771_x_at 60 NM_020975/ NM_020630/ RET, Hs.350321,1026 1143 RET, Hs.350321, 216139_s_at 61 NM_033392/ NM_015133/ MAPK8IP3,Hs.207763, 1057 1138 MAPK8IP3, Hs.207763, 216902_s_at 62 NM_018427/ RRN3Hs.460078 1010 208265_at 63 NM_020161/ DKFZP547H025 Hs.283092 1019209456_s_at 64 NM_033645/ NM_033644/ NM_012300/ FBXW11, Hs.484138, 10591148 1193 FBXW11, Hs.484138, FBXW11, Hs.484138, 217237_at 65 —/ — —217208_s_at 66 NM_004087/ DLG1 Hs.292549 885 221757_at 67 NM_052880/MGC17330 Hs.26670 1060 213481_at 68 —/ — — 219025_at 69 NM_020404/CD164L1 Hs.195727 1021 215201_at 70 —/ — — 205378_s_at 71 NM_000665/NM_015831/ ACHE, Hs.154495, 833 1139 ACHE, Hs.154495, 219829_at 72NM_012278/ ITGB1BP2 Hs.109999 947 216908_x_at 73 NM_018427/ NM_145237/RRN3, Hs.460078, 1010 1156 LOC94431, Hs.546468, 217184_s_at 74NM_206961/ NM_002344/ LTK, Hs.434481, 1105 1121 LTK, Hs.434481,211181_x_at 75 NM_001001890/ NM_001754/ RUNX1, Hs.149261, 843 1179RUNX1, Hs.149261, 214958_s_at 76 NM_007267/ EVER1 Hs.16165 938 220369_at77 NM_017936/ KIAA2010 Hs.533887 998 211848_s_at 78 NM_006890/ CEACAM7Hs.74466 932 221638_s_at 79 NM_003763/ NM_001001434/ NM_001001433/STX16, Hs.307913, 880 842 1181 STX16, Hs.307913, STX16, Hs.307913,221723_s_at 80 NM_021196/ NM_133479/ NM_133478/ NM_033323/ SLC4A5,Hs.469033, 1028 1152 1201 1223 SLC4A5, Hs.469033, SLC4A5, Hs.469033,SLC4A5, Hs.469033, 201380_at 81 NM_006371/ CRTAP Hs.517888 923 34063_at82 NM_001003715/ NM_001003716/ NM_004259/ RECQL5, Hs.514480, 845 11781191 RECQL5, Hs.514480, RECQL5, Hs.514480, 214757_at 83 —/ — — 218176_at84 NM_022149/ MAGEF1 Hs.306123 1034 221977_at 85 —/ — — 214161_at 86 —/— — 214857_at 87 —/ — — 216230_x_at 88 NM_000543/ NM_001007593/ SMPD1,Hs.498173, 829 1118 SMPD1, Hs.498173, 205019_s_at 89 NM_004624/ VIPR1Hs.348500 893 221707_s_at 90 NM_018289/ FLJ10979 Hs.461819 1006208664_s_at 91 NM_001001894/ NM_003316/ TTC3, Hs.368214, 844 1180 TTC3,Hs.368214, 215167_at 92 —/ — — 215437_x_at 93 NM_013449/ BAZ2A Hs.314263955 210892_s_at 94 NM_001518/ NM_033001/ NM_033000/ NM_032999/ GTF2I,Hs.520459, 854 1146 1198 1222 GTF2I, Hs.520459, GTF2I, Hs.520459, GTF2I,Hs.520459, 212400_at 95 NM_203305/ EEIG1 Hs.460208 1101 215137_at 96 —/— — 205750_at 97 NM_004332/ BPHL Hs.10136 888 210628_x_at 98 NM_003573/LTBP4 Hs.466766 877 218210_at 99 NM_024619/ FN3KRP Hs.31431 1050216784_at 100 —/ — — 201819_at 101 NM_005505/ SCARB1 Hs.298813 911214312_at 102 —/ — — 215556_at 103 —/ — — 221756_at 104 NM_052880/MGC17330 Hs.26670 1060 216909_at 105 —/ — — 220249_at 106 NM_012269/HYAL4 Hs.28673 946 211272_s_at 107 NM_201554/ NM_001345/ NM_201445/NM_201444/ DGKA, Hs.524488, 1098 1119 1211 1229 DGKA, Hs.524488, DGKA,Hs.524488, DGKA, Hs.524488, 218651_s_at 108 NM_018357/ FLJ11196Hs.416755 1008 218285_s_at 109 NM_020139/ DHRS6 Hs.124696 1018 217385_at110 —/ — — 202894_at 111 NM_004444/ EPHB4 Hs.437008 890 217631_at 112 —/— — 220487_at 113 NM_018968/ SNTG2 Hs.148819 1015 203579_s_at 114NM_003983/ SLC7A6 Hs.351571 884 215412_x_at 115 NM_005395/ NM_001003686/NM_001003687/ NM_174930/ NM_002679/ NM_000535/ PMS2L3, Hs.549057, 9081115 1183 1086 867 828 PMS2L3, Hs.549057, PMS2L3, Hs.549057, PMS2L5,Hs.397073, POM121, Hs.488624, PMS2, Hs.487470, 212217_at 116 —/ — —221602_s_at 117 NM_005449/ TOSO Hs.58831 909 217847_s_at 118 NM_005119/THRAP3 Hs.160211 905 215275_at 119 —/ — — 221951_at 120 NM_174940/LOC283232 Hs.448664 1087 213224_s_at 121 —/ — — 218967_s_at 122NM_030664/ NM_001001484/ PTER, Hs.444321, 1055 1113 PTER, Hs.444321,208442_s_at 123 NM_138292/ NM_000051/ ATM, Hs.435561, 1069 1109 ATM,Hs.435561, 203675_at 124 NM_005013/ NUCB2 Hs.128686 900 207105_s_at 125NM_005027/ PIK3R2 Hs.371344 901 219144_at 126 NM_024025/ MGC1136 Hs.87191042 212463_at 127 NM_000611/ NM_203331/ NM_203329/ NM_203330/ CD59,Hs.278573, 831 1175 1212 1230 CD59, Hs.278573, CD59, Hs.278573, CD59,Hs.278573, 202040_s_at 128 NM_005056/ JARID1A Hs.76272 902 64432_at 129NM_016534/ FLJ39616 Hs.333120 991 200965_s_at 130 NM_006720/ NM_002313/NM_001003407/ NM_001003408/ ABLIM1, Hs.438236, 930 1120 1187 1232ABLIM1, Hs.438236, ABLIM1, Hs.438236, ABLIM1, Hs.438236, 205353_s_at 131NM_002567/ PBP Hs.433863 866 213177_at 132 NM_033392/ NM_015133/MAPK8IP3, Hs.207763, 1057 1138 MAPK8IP3, Hs.207763, 218373_at 133NM_022476/ FTS Hs.380897 1040 208333_at 134 NM_022363/ LHX5 Hs.3020291039 206150_at 135 NM_001242/ TNFRSF7 Hs.355307 851 202431_s_at 136NM_002467/ MYC Hs.202453 863 207838_x_at 137 NM_020524/ PBXIP1 Hs.5058061023 218325_s_at 138 NM_080797/ NM_080796/ NM_022105/ DATF1, Hs.551527,1062 1149 1197 DATF1, Hs.551527, DATF1, Hs.551527, 218475_at 139NM_182984/ NM_022727/ HTF9C, Hs.549133, 1090 1144 HTF9C, Hs.549133,218670_at 140 NM_025215/ PUS1 Hs.507295 1053 205594_at 141 NM_014897/ZNF652 Hs.463375 967 215411_s_at 142 NM_147200/ NM_147686/ C6ORF4,Hs.486228, 1076 1160 C6ORF4, Hs.486228, 203048_s_at 143 NM_014639/KIAA0372 Hs.482868 962 216885_s_at 144 NM_015726/ WDR42A Hs.492236 982219767_s_at 145 NM_005111/ NM_145311/ NM_145858/ CRYZL1, Hs.352671, 9031157 1202 CRYZL1, Hs.352671, CRYZL1, Hs.352671, 219131_at 146 NM_013319/TERE1 Hs.522933 953 213176_s_at 147 NM_003573/ LTBP4 Hs.466766 877208661_s_at 148 NM_001001894/ NM_003316/ TTC3, Hs.368214, 844 1180 TTC3,Hs.368214, 208196_x_at 149 NM_172388/ NM_172389/ NM_172387/ NM_006162/NFATC1, Hs.534074, 1083 1164 1206 1220 NFATC1, Hs.534074, NFATC1,Hs.534074, NFATC1, Hs.534074, 212178_s_at 150 NM_172020/ POM121Hs.488624 1081 221601_s_at 151 NM_005449/ TOSO Hs.58831 909 222013_x_at152 NM_152563/ NM_032916/ NM_018172/ FLJ10661, Hs.61142, 1077 1145 1196MGC16279, Hs.458413, FLJ10661, Hs.61142, 202524_s_at 153 NM_014767/SPOCK2 Hs.523009 963 212068_s_at 154 —/ — — 202830_s_at 155 NM_001467/SLC37A4 Hs.132760 853 209835_x_at 156 NM_001001391/ NM_001001390/NM_001001389/ NM_000610/ NM_001001392/ CD44, Hs.502328, 841 1177 11861231 1233 CD44, Hs.502328, CD44, Hs.502328, CD44, Hs.502328, CD44,Hs.502328, 212257_s_at 157 NM_139045/ NM_003070/ SMARCA2, Hs.298990,1071 1124 SMARCA2, Hs.298990, 212071_s_at 158 —/ — — 213322_at 159NM_145063/ C6ORF130 Hs.549281 1075 210645_s_at 160 NM_001001894/NM_003316/ TTC3, Hs.368214, 844 1180 TTC3, Hs.368214, 202514_at 161 —/ —— 217122_s_at 162 NM_014854/ SLC35E2 Hs.551612 964 218440_at 163NM_020166/ MCCC1 Hs.47649 1020 210707_x_at 164 NM_174930/ NM_002679/NM_005395/ NM_001003686/ NM_001003687/ NM_000535/ PMS2L5, Hs.397073,1086 867 908 1115 1183 828 POM121, Hs.488624, PMS2L3, Hs.549057, PMS2L3,Hs.549057, PMS2L3, Hs.549057, PMS2, Hs.487470, 61734_at 165 NM_020650/RCN3 Hs.439184 1024 221500_s_at 166 NM_001001434/ NM_003763/NM_001001433/ STX16, Hs.307913, 842 880 1181 STX16, Hs.307913, STX16,Hs.307913, 219422_at 167 —/ — — 222244_s_at 168 NM_017903/ FLJ20618Hs.551545 996 212550_at 169 NM_012448/ STAT5B Hs.132864 950 206544_x_at170 NM_139045/ NM_003070/ SMARCA2, Hs.298990, 1071 1124 SMARCA2,Hs.298990, 216380_x_at 171 NM_001031/ RPS28 Hs.546293 847 203408_s_at172 NM_002971/ SATB1 Hs.517717 870 218258_at 173 NM_015972/ MGC9850Hs.507584 984 212234_at 174 NM_015338/ ASXL1 Hs.374043 976 217461_x_at175 NM_001207/ BTF3 Hs.529798 849 218428_s_at 176 NM_016316/ REV1LHs.443077 989 215667_x_at 177 NM_002679/ NM_174930/ NM_005395/NM_001003686/ NM_001003687/ POM121, Hs.488624, 867 1086 908 1115 1183PMS2L5, Hs.397073, PMS2L3, Hs.549057, PMS2L3, Hs.549057, PMS2L3,Hs.549057, 220465_at 178 —/ — — 217988_at 179 NM_021178/ NM_182852/NM_182851/ NM_182849/ CCNB1IP1, Hs.107003, 1027 1169 1208 1227 CCNB1IP1,Hs.107003, CCNB1IP1, Hs.107003, CCNB1IP1, Hs.107003, 221981_s_at 180NM_030581/ FLJ12270 Hs.280951 1054 212201_at 181 —/ — — 208795_s_at 182NM_005916/ NM_182776/ MCM7, Hs.438720, 916 1168 MCM7, Hs.438720,208336_s_at 183 NM_004868/ NM_138501/ GPSN2, Hs.515642, 898 1153 GPSN2,Hs.515642, 221499_s_at 184 NM_001001434/ NM_003763/ NM_001001433/ STX16,Hs.307913, 842 880 1181 STX16, Hs.307913, STX16, Hs.307913, 202167_s_at185 NM_022362/ MMS19L Hs.500721 1038 201065_s_at 186 NR_002206/NM_001518/ NM_033001/ NM_033000/ NM_032999/ —, —, 1107 854 1146 11981222 GTF2I, Hs.520459, GTF2I, Hs.520459, GTF2I, Hs.520459, GTF2I,Hs.520459, 211172_x_at 187 NM_004842/ NM_138633/ NM_016377/ AKAP7,Hs.486483, 896 1154 1194 AKAP7, Hs.486483, AKAP7, Hs.486483, 218707_at188 NM_018337/ ZNF444 Hs.24545 1007 206770_s_at 189 NM_012243/ SLC35A3Hs.448979 945 200898_s_at 190 NM_012215/ MGEA5 Hs.500842 943 215519_x_at191 NM_015705/ RUTBC3 Hs.474914 981 212406_s_at 192 NM_018257/ C20ORF36Hs.473317 1005 210826_x_at 193 NM_133341/ NM_133339/ NM_133340/NM_133344/ NM_133342/ NM_133343/ NM_133338/ NM_002873/ RAD17, Hs.16184,1066 1151 1200 1224 1237 1239 1243 1246 RAD17, Hs.16184, RAD17,Hs.16184, RAD17, Hs.16184, RAD17, Hs.16184, RAD17, Hs.16184, RAD17,Hs.16184, RAD17, Hs.16184, 218444_at 194 NM_024105/ ALG12 Hs.526711 1043221822_at 195 NM_138414/ LOC112869 Hs.460487 1070 220755_s_at 196NM_016947/ C6ORF48 Hs.109798 992 218970_s_at 197 NM_015960/ CUTCHs.16606 983 218253_s_at 198 NM_006893/ LGTN Hs.497581 933 221293_s_at199 NM_022047/ DEF6 Hs.15476 1032 217742_s_at 200 NM_100486/ NM_016628/NM_100264/ WAC, Hs.435610, 1063 1140 1199 WAC, Hs.435610, WAC,Hs.435610, 207127_s_at 201 NM_021644/ NM_012207/ HNRPH3, Hs.499891, 10301136 HNRPH3, Hs.499891, 217850_at 202 NM_206826/ NM_014366/ NM_206825/GNL3, Hs.313544, 1104 1137 1213 GNL3, Hs.313544, GNL3, Hs.313544,212505_s_at 203 NM_015329/ KIAA0892 Hs.112751 974 211971_s_at 204NM_133259/ LRPPRC Hs.368084 1065 216387_x_at 205 NM_013269/NM_001004420/ NM_001004419/ NM_002520/ OCIL, Hs.268326, 952 1117 11851218 OCIL, Hs.268326, OCIL, Hs.268326, NPM1, Hs.519452, 218152_at 206NM_018200/ HMG20A Hs.69594 1002 201788_at 207 NM_203499/ NM_007372/DDX42, Hs.8765, 1102 1135 DDX42, Hs.8765, 201922_at 208 NM_014886/ TINP1Hs.482526 966 212982_at 209 NM_015336/ ZDHHC17 Hs.4014 975 214173_x_at210 NM_134447/ NM_003796/ C19ORF2, Hs.466391, 1068 1128 C19ORF2,Hs.466391, 211937_at 211 NM_001417/ EIF4B Hs.512629 852 216843_x_at 212NM_000535/ NM_174930/ NM_002679/ NM_005395/ NM_001003686/ NM_001003687/NM_032958/ NM_032959/ PMS2, Hs.487470, 828 1086 867 908 1115 1183 12421247 PMS2, Hs.397073, L5, Hs.488624, POM121, Hs.549057, PMS2L3,Hs.549057, PMS2L3, Hs.549057, PMS2L3, Hs.433879, POLR2J2, Hs.433879,POLR2J2, 212854_x_at 213 NM_032264/ NM_173638/ NM_183372/ AE2,Hs.325422, 1056 1166 1209 MGC8902, Hs.512037, LOC200030, Hs.515837,212886_at 214 NM_015621/ DKFZP434C171 Hs.132994 978 220607_x_at 215NM_016397/ NM_198976/ TH1L, Hs.517148, 990 1172 TH1L, Hs.517148,212132_at 216 NM_015578/ C19ORF13 Hs.407368 977 214042_s_at 217NM_000983/ RPL22 Hs.515329 839 212660_at 218 NM_015288/ PHF15 Hs.483419972 208944_at 219 —/ — — 210011_s_at 220 NM_013986/ NM_005243/ EWSR1,Hs.374477, 956 1130 EWSR1, Hs.374477, 211938_at 221 NM_001417/ EIF4BHs.512629 852 220408_x_at 222 NM_017569/ FAM48A Hs.435815 994 212114_at223 —/ — — 212455_at 224 NM_133370/ YT521 Hs.175955 1067 212299_at 225—/ — — 200005_at 226 NM_003753/ EIF3S7 Hs.55682 879 200081_s_at 227NM_001010/ RPS6 Hs.408073 846 213687_s_at 228 NM_000996/ RPL35AHs.529631 840 204102_s_at 229 NM_001961/ EEF2 Hs.515070 859 211666_x_at230 NM_000967/ RPL3 Hs.119598 836 209134_s_at 231 NM_001010/ RPS6Hs.408073 846 221700_s_at 232 NM_003333/ UBA52 Hs.5308 876 200034_s_at233 NM_000970/ RPL6 Hs.528668 837 201254_x_at 234 NM_001010/ RPS6Hs.408073 846 212734_x_at 235 NM_000977/ NM_033251/ RPL13, Hs.410817,838 1147 RPL13, Hs.410817, 217718_s_at 236 NM_139323/ NM_003404/ YWHAB,Hs.279920, 1073 1126 YWHAB, Hs.279920, 208678_at 237 NM_001696/ ATP6V1E1Hs.517338 855 200633_at 238 NM_018955/ UBB Hs.356190 1014 201318_s_at239 NM_033546/ NM_006471/ MRLC2, Hs.464472, 1058 1134 MRCL3, Hs.190086,202090_s_at 240 NM_006830/ UQCR Hs.8372 931 221474_at 241 NM_033546/MRLC2 Hs.464472 1058 214629_x_at 242 NM_153828/ NM_207520/ NM_207521/NM_020532/ NM_007008/ RTN4, Hs.429581, 1080 1176 1214 1221 1236 RTN4,Hs.429581, RTN4, Hs.429581, RTN4, Hs.429581, RTN4, Hs.429581,200067_x_at 243 NM_152827/ NM_003795/ NM_152828/ SNX3, Hs.12102, 10781127 1203 SNX3, Hs.12102, SNX3, Hs.12102, 201899_s_at 244 NM_181762/NM_003336/ NM_181777/ UBE2A, Hs.379466, 1089 1125 1207 UBE2A, Hs.379466,UBE2A, Hs.379466, 210968_s_at 245 NM_153828/ NM_207520/ NM_207521/NM_020532/ NM_007008/ RTN4, Hs.429581, 1080 1176 1214 1221 1236 RTN4,Hs.429581, RTN4, Hs.429581, RTN4, Hs.429581, RTN4, Hs.429581,200609_s_at 246 NM_005112/ NM_017491/ WDR1, Hs.128548, 904 1142 WDR1,Hs.128548, 208805_at 247 NM_002791/ PSMA6 Hs.446260 868 218571_s_at 248NM_014169/ C14ORF123 Hs.279761 957 217730_at 249 NM_022152/ PP1201Hs.98475 1035 218520_at 250 NM_013254/ TBK1 Hs.505874 951 208908_s_at251 NM_173061/ NM_173062/ NM_173060/ NM_001750/ CAST, Hs.440961, 10851165 1084 1217 CAST, Hs.440961, CAST, Hs.440961, CAST, Hs.440961,207467_x_at 252 NM_173061/ NM_173062/ NM_173060/ NM_001750/ CAST,Hs.440961, 1085 1165 1084 1217 CAST, Hs.440961, CAST, Hs.440961, CAST,Hs.440961, 201975_at 253 NM_198240/ NM_002956/ RSN, Hs.524809, 1093 1123RSN, Hs.524809, 200814_at 254 NM_006263/ NM_176783/ PSME1, Hs.75348, 9201167 PSME1, Hs.75348, 203090_at 255 NM_006923/ SDF2 Hs.514036 934201470_at 256 NM_004832/ GSTO1 Hs.190028 895 212586_at 257 NM_173060/CAST Hs.440961 1084 200703_at 258 NM_003746/ DNCL1 Hs.5120 878 217995_at259 NM_021199/ SQRDL Hs.511251 1029 201346_at 260 NM_024551/ ADIPOR2Hs.371642 1048 201609_x_at 261 NM_012405/ NM_170705/ ICMT, Hs.515688,949 1162 ICMT, Hs.515688, 202000_at 262 NM_002490/ NDUFA6 Hs.274416 864202001_s_at 263 NM_002490/ NDUFA6 Hs.274416 864 203880_at 264 NM_005694/COX17 Hs.534383 914 218525_s_at 265 NM_017902/ HIF1AN Hs.500788 995219798_s_at 266 NM_019606/ FLJ20257 Hs.178011 1017 208398_s_at 267NM_004865/ TBPL1 Hs.486507 897 218358_at 268 NM_024324/ MGC11256Hs.211282 1045 203097_s_at 269 —/ — — 221598_s_at 270 NM_004269/ CRS98Hs.374262 887 209546_s_at 271 AF323540/ GenBank Hs.114309 811 50400_at272 AI743990/ GenBank Hs.24859 812 217752_s_at 273 NM_018235/ GenBankHs.273230 1003 201931_at 274 NM_000126/ GenBank Hs.169919 825218567_x_at 275 NM_005700/ GenBank Hs.22880 915 202056_at 276 AW051311/GenBank Hs.169149 816 218907_s_at 277 NM_023942/ GenBank Hs.284135 1041213726_x_at 278 AA515698/ GenBank Hs.251653 806 204448_s_at 279AF031463/ GenBank Hs.9302 808 1405_i_at 280 M21121/ GenBank — 823212864_at 281 Y16521/ GenBank Hs.24812 1108 209444_at 282 BC001851/GenBank Hs.7940 819 208898_at 283 AF077614/ GenBank Hs.272630 809202377_at 284 AW026535/ GenBank Hs.23581 815 209547_s_at 285 BC001043/GenBank Hs.15075 818 202922_at 286 BF676980/ GenBank Hs.151393 821201403_s_at 287 NM_004528/ GenBank Hs.111811 892 213154_s_at 288AI934125/ GenBank Hs.17411 814 215676_at 289 N91109/ GenBank Hs.32935824 218927_s_at 290 NM_018641/ GenBank Hs.25204 1012 213648_at 291AW614427/ GenBank Hs.182877 817 209593_s_at 292 AF317129/ GenBankHs.252682 810 203731_s_at 293 NM_014569/ GenBank Hs.110839 960 201234_at294 NM_004517/ GenBank Hs.6196 891 214817_at 295 BE783668/ GenBankHs.175780 820 201761_at 296 NM_006636/ GenBank Hs.154672 929 205467_at297 NM_001230/ GenBank Hs.5353 850 222318_at 298 AI744673/ GenBankHs.186970 813 209933_s_at 299 AF020314/ GenBank Hs.9688 807 200734_s_at300 BG341906/ GenBank Hs.119177 822 219899_x_at 301 NM_014434/ NDOR1Hs.512564 959 221563_at 302 NM_144729/ NM_144728/ NM_007207/ DUSP10,Hs.497822, 1074 1155 1192 DUSP10, Hs.497822, DUSP10, Hs.497822, 65517_at303 NM_005498/ AP1M2 Hs.18894 910 205126_at 304 NM_006296/ VRK2Hs.468623 921 200696_s_at 305 NM_198252/ NM_000177/ GSN, Hs.522373, 10941110 GSN, Hs.522373, 208790_s_at 306 NM_012232/ PTRF Hs.437191 944205115_s_at 307 NM_016196/ RBM19 Hs.7482 987 213982_s_at 308 NM_014857/RABGAP1L Hs.495391 965 206992_s_at 309 NM_015684/ NM_001003805/NM_001003803/ ATP5S, Hs.438489, 980 1116 1184 ATP5S, Hs.438489, ATP5S,Hs.438489, 201060_x_at 310 NM_198194/ NM_004099/ NM_017723/ STOM,Hs.253903, 1092 1129 1195 STOM, Hs.253903, FLJ20245, Hs.495541,209278_s_at 311 NM_006528/ TFPI2 Hs.438231 924 210542_s_at 312 —/ — —202006_at 313 NM_002835/ PTPN12 Hs.61812 869 210557_x_at 314 NM_172211/NM_000757/ NM_172210/ NM_172212/ CSF1, Hs.173894, 1082 1112 1205 1226CSF1, Hs.173894, CSF1, Hs.173894, CSF1, Hs.173894, 210796_x_at 315NM_198846/ NM_198845/ NM_001245/ SIGLEC6, Hs.397255, 1097 1171 1188SIGLEC6, Hs.397255, SIGLEC6, Hs.397255, 220825_s_at 316 NM_018240/KIRREL Hs.272234 1004 202378_s_at 317 NM_017526/ LEPR Hs.23581 993210241_s_at 318 NM_007233/ TP53AP1 Hs.274329 936 213069_at 319 —/ — —216034_at 320 NM_080740/ SUHW1 Hs.178665 1061 210793_s_at 321 NM_139131/NM_005387/ NUP98, Hs.524750, 1072 1131 NUP98, Hs.524750, 207375_s_at 322NM_002189/ NM_172200/ IL15RA, Hs.524117, 860 1163 IL15RA, Hs.524117,206247_at 323 NM_005931/ MICB Hs.211580 917 217078_s_at 324 NM_007261/CMRF- Hs.9688 937 35H 219257_s_at 325 NM_021972/ NM_182965/ SPHK1,Hs.68061, 1031 1170 SPHK1, Hs.68061, 204781_s_at 326 NM_152876/NM_152877/ NM_152874/ NM_152875/ NM_152873/ NM_152871/ NM_152872/NM_000043/ FAS, Hs.244139, 1079 1161 1204 1225 1238 1240 1244 1245 FAS,Hs.244139, FAS, Hs.244139, FAS, Hs.244139, FAS, Hs.244139, FAS,Hs.244139, FAS, Hs.244139, FAS, Hs.244139, 221536_s_at 327 NM_018385/FLJ11301 Hs.518505 1009 209468_at 328 NM_002335/ LRP5 Hs.6347 861201061_s_at 329 NM_198194/ NM_004099 STOM, Hs.253903, 1092 1129 STOM,Hs.253903, 203499_at 330 NM_004431/ EPHA2 Hs.171596 889 213324_at 331NM_198291/ NM_005417/ SRC, Hs.195659, 1095 1132 SRC, Hs.195659,221535_at 332 NM_018385/ FLJ11301 Hs.518505 1009 219938_s_at 333NM_024430/ PSTPIP2 Hs.368623 1046 213787_s_at 334 NM_006579/ EBPHs.522636 926 219592_at 335 NM_024596/ MCPH1 Hs.550532 1049 200637_s_at336 NM_130440/ NM_002840/ PTPRF, Hs.272062, 1064 1122 PTPRF, Hs.272062,202193_at 337 NM_005569/ NM_016733/ LIMK2, Hs.474596, 913 1141 LIMK2,Hs.474596, 214859_at 338 NM_015082/ FSTL4 Hs.483390 969 209213_at 339NM_001757/ CBR1 Hs.88778 857 218945_at 340 NM_024109/ MGC2654 Hs.3063801044 220471_s_at 341 NM_025107/ MYCT1 Hs.18160 1052 59625_at 342NM_003946/ NOL3 Hs.513667 883 207233_s_at 343 NM_198158/ NM_000248/NM_198178/ NM_198177/ NM_006722/ NM_198159/ MITF, Hs.166017, 1091 11111210 1228 1235 1241 MITF, Hs.166017, MITF, Hs.166017, MITF, Hs.166017,MITF, Hs.166017, MITF, Hs.166017, 214070_s_at 344 —/ — — 219785_s_at 345—/ — — 220684_at 346 NM_013351/ TBX21 Hs.272409 954 202245_at 347NM_002340/ LSS Hs.517366 862 207298_at 348 NM_006632/ SLC17A3 Hs.327179927 220201_at 349 NM_018835/ MNAB Hs.533499 1013 203208_s_at 350NM_014637/ CHPPR Hs.521608 961 207033_at 351 NM_005142/ GIF Hs.110014906 204929_s_at 352 NM_006634/ VAMP5 Hs.172684 928 209735_at 353NM_004827/ ABCG2 Hs.480218 894 209234_at 354 NM_015074/ KIF1B Hs.97858968 210102_at 355 NM_198315/ LOH11CR2A Hs.152944 1096 204114_at 356NM_007361/ NID2 Hs.369840 941 203344_s_at 357 NM_203292/ NM_203291/NM_002894/ RBBP8, Hs.546282, 1100 1174 1190 RBBP8, Hs.546282, RBBP8,Hs.546282, 216891_at 358 —/ — — 221680_s_at 359 NM_016135/ ETV7Hs.272398 986 202087_s_at 360 NM_001912/ NM_145918/ CTSL, Hs.418123, 8581159 CTSL, Hs.418123, 213324_at 331 NM_198291/ NM_005417/ SRC,Hs.195659, 1095 1132 SRC, Hs.195659, 221535_at 332 NM_018385/ FLJ11301Hs.518505 1009 219938_s_at 333 NM_024430/ PSTPIP2 Hs.368623 1046213787_s_at 334 NM_006579/ EBP Hs.522636 926 219592_at 335 NM_024596/MCPH1 Hs.550532 1049 200637_s_at 336 NM_130440/ NM_002840/ PTPRF,Hs.272062, 1064 1122 PTPRF, Hs.272062, 202193_at 337 NM_005569/NM_016733/ LIMK 2, Hs.474596, 913 1141 LIMK 2, Hs.474596, 214859_at 338NM_015082/ FSTL4 Hs.483390 969 209213_at 339 NM_001757/ CBR1 Hs.88778857 218945_at 340 NM_024109/ MGC2654 Hs.306380 1044 220471_s_at 341NM_025107/ MYCT1 Hs.18160 1052 59625_at 342 NM_003946/ NOL3 Hs.513667883 207233_s_at 343 NM_198158/ NM_000248/ NM_198178/ NM_198177/NM_006722/ NM_198159/ MITF, Hs.166017, 1091 1111 1210 1228 1235 1241MITF, Hs.166017, MITF, Hs.166017, MITF, Hs.166017, MITF, Hs.166017,MITF, Hs.166017, 214070_s_at 344 —/ — — 219785_s_at 345 —/ — — 220684_at346 NM_013351/ TBX21 Hs.272409 954 202245_at 347 NM_002340/ LSSHs.517366 862 207298_at 348 NM_006632/ SLC17A3 Hs.327179 927 220201_at349 NM_018835/ MNAB Hs.533499 1013 203208_s_at 350 NM_014637/ CHPPRHs.521608 961 207033_at 351 NM_005142/ GIF Hs.110014 906 204929_s_at 352NM_006634/ VAMP5 Hs.172684 928 209735_at 353 NM_004827/ ABCG2 Hs.480218894 209234_at 354 NM_015074/ KIF1B Hs.97858 968 210102_at 355 NM_198315/LOH11CR2A Hs.152944 1096 204114_at 356 NM_007361/ NID2 Hs.369840 941203344_s_at 357 NM_203292/ NM_203291/ NM_002894 RBBP8, Hs.546282, 11001174 1190 RBBP8, Hs.546282, RBBP8, Hs.546282, 216891_at 358 —/ — —221680_s_at 359 NM_016135/ ETV7 Hs.272398 986 202087_s_at 360 NM_001912/NM_145918/ CTSL, Hs.418123, 858 1159 CTSL, Hs.418123, 210073_at 391NM_003034/ SIAT8A Hs.408614 871 209524_at 392 NM_016073/ HDGFRP3Hs.513954 985 219759_at 393 NM_022350/ LRAP Hs.482910 1036 202112_at 394NM_000552/ VWF Hs.440848 830 219410_at 395 NM_018004/ FLJ10134 Hs.1265981000 203819_s_at 396 NM_006547/ IMP-3 Hs.432616 925 212730_at 397NM_015286/ NM_145728/ DMN, Hs.207106, 971 1158 DMN, Hs.207106, 220122_at398 —/ — — 208782_at 399 NM_007085/ FSTL1 Hs.269512 935 202468_s_at 400NM_003798/ CTNNAL1 Hs.58488 882 207018_s_at 401 NM_004163/ RAB27BHs.25318 886 210354_at 402 NM_000619/ IFNG Hs.856 832 201110_s_at 403NM_003246/ THBS1 Hs.164226 874 207808_s_at 404 NM_000313/ PROS1 Hs.64016827 205612_at 405 NM_007351/ MMRN1 Hs.268107 940 214073_at 406 —/ — —

The genes encoding RNA polymerase I transcription factor (RRN3) andleucine-rich PPR-motif containing protein (LRPRC) were found as mostsignificantly down-regulated genes in BMS signature (Table 1,hereinabove). RRN33 (transcription initiation factor TIF-IA), a 72-kDaprotein, is essential for ribosomal DNA (rDNA) transcription and acts asa bridge between RNA pol I and the committed rDNA promoter(Hirschler-Laszkiewicz I, et al., 2003; Miller G, et al., 2001;20:1373-1382). The suppression of polymerase I regulation mechanism isconfirmed by down-regulation of polymerase (RNA) I polypeptide D(POLR1D).

LRPPRC is a candidate gene for the French-Canadian type of Leighsyndrome, a form of cytochrome c oxidase deficiency, and plays a role intranslation or stability of mitochondrially encoded cytochrome c oxidase(COX) subunits (Mootha V K, et al., 2003). The LRPPC together withPOLR1D molecules comprise a complex with NFkBIB protein (Bouwmeester T,et al., 2004) that inhibits proinflammatory NFkB pathway.

Without being bound by any theory, the suppression of molecules involvedin polymerase I related mechanism, COXI and NFkB regulation couldaccount for the differences between BMS and typical RRMS patients. Inaddition, the polymerase I related mechanism can be potential drugtargets for the treatment of RRMS aimed to switch RRMS to the BMSvariant. One of commercially available drug that has proven effects onpolymerase I mechanism is a diterpenoid triepoxide Triptolide (TPT),isolated from the Chinese herb Tripterygium wilfordii (Leuenroth S J andCrews C M. Triptolide-induced transcriptional arrest is associated withchanges in nuclear substructure. Cancer Res. 2008; 68:5257-5266).Triptolide has various anti-inflammatory effects (Liu Y, et al.Triptolide, a component of Chinese herbal medicine, modulates thefunctional phenotype of dendritic cells. Transplantation. 2007;84:1517-1526), it modulates T-cell inflammatory responses andameliorates Experimental Autoimmune Encephalomyelitis (Wang Y, et al.Triptolide modulates T-cell inflammatory responses and amelioratesexperimental autoimmune encephalomyelitis. J Neurosci Res. 2008;86:2441-2449).

More specifically TPT demonstrated to suppress of T lymphocyte functionincluding T cell apoptosis induction, inhibition of lymphocyteprolipheration and IFNγ production (Chen B J. 2001. Triptolide, a novelimmunosuppressive and anti-inflammatory agent purified from a Chineseherb Tripterygium wilfordii Hook f. Leuk Lymphoma 42:253-265; Qiu D, KaoP N. 2003 Immunosuppressive and anti-inflammatory mechanisms oftriptolide, the principal active diterpenoid from the Chinese medicinalherb Tripterygium wilfordii Hook f. Drugs R D 4:1-18; Yang Y, Liu Z,Tolosa E, Yang J, Li L. 1998. Triptolide induces apoptotic death of Tlymphocyte. Immunopharmacology 40:139-149; Chan M A, Kohlmeier J E,Branden M, Jung M, Benedict S H. 1999. Triptolide is more effective inpreventing T cell proliferation and interferon-gamma production than isFK506. Phytother Res 13:464-467). The TPT decreased IL2 and IL2 receptorexpression by inhibiting activation of the purine box regulator of theNFkB of activated T cells (Qiu 1999). Additionally, it was demonstratedthat TPT can inhibit the maturation, antigen processing, andpresentation of dendritic cells and can suppress tumor necrosis factor(TNF)-a and IL-6 production by activated macrophages (Zhu K J, Shen Q Y,Cheng H, Mao X H, Lao L M, Hao G L. 2005. Triptolide affects thedifferentiation, maturation and function of human dendritic cells. IntImmunopharmacol 5:1415-1426; Wu Y, Cui J, Bao X, Chan S, Young D O, LiuD, Shen P. 2006. Triptolide attenuates oxidative stress, NF-kappaBactivation and multiple cytokine gene expression in murine peritonealmacrophage. Int J Mol Med 17:141-150).

Table 3, hereinbelow, discloses the genes involved in the RNA polymeraseI pathway, which are likely to be involved in typical RRMS or BMSpathology.

TABLE 3 Genes involved in the RNA polymerase I pathway SEQRepresentative Affymetrix ID Public ID/SEQ ID ProbSet NO: NO: GeneSymbol Gene Title 216902_s_at 62 AF001549/1284; RRN3 RRN3 RNA polymeraseI NM_018427/1285 transcription factor homolog 211971_s_at 204AI653608/1286; LRPPRC leucine-rich PPR-motif NM_133259/1287 containing220113_x_at 1248 NM_019014/1288 POLR1B polymerase (RNA) I polypeptide B,128 kDa 207515_s_at 1249 NM_004875/1289 POLR1C polymerase (RNA) Ipolypeptide C, 30 kDa 209317_at 1250 AF008442/1290 POLR1C polymerase(RNA) I polypeptide C, 30 kDa 218258_at 173 NM_015972/1291 POLR1Dpolymerase (RNA) I polypeptide D, 16 kDa 202725_at 1251 NM_000937/1292POLR2A polymerase (RNA) II (DNA directed) polypeptide A, 220 kDa217420_s_at 1252 M21610/1293 POLR2A polymerase (RNA) II (DNA directed)polypeptide A, 220 kDa 201803_at 1253 NM_000938/1294 POLR2B polymerase(RNA) II (DNA directed) polypeptide B, 140 kDa 208996_s_at 1254BC000409/1295 POLR2C polymerase (RNA) II (DNA directed) polypeptide C,33 kDa 214263_x_at 1255 AI192781/1296 POLR2C polymerase (RNA) II (DNAdirected) polypeptide C, 33 kDa 216282_x_at 1256 AJ224143/1297 POLR2Cpolymerase (RNA) II (DNA directed) polypeptide C, 33 kDa 203664_s_at1257 NM_004805/1298 POLR2D polymerase (RNA) II (DNA directed)polypeptide D 214144_at 1258 BF432147/1299 POLR2D polymerase (RNA) II(DNA directed) polypeptide D 213887_s_at 1259 AI554759/1300 POLR2Epolymerase (RNA) II (DNA directed) polypeptide E, 25 kDa 217854_s_at1260 BC004441/1301 POLR2E polymerase (RNA) II (DNA directed) polypeptideE, 25 kDa 209511_at 1261 BC003582/1302 POLR2F polymerase (RNA) II (DNAdirected) polypeptide F 202306_at 1262 NM_002696/1303 POLR2G polymerase(RNA) II (DNA directed) polypeptide G 209302_at 1263 U37689/1304 POLR2Hpolymerase (RNA) II (DNA directed) polypeptide H 212955_s_at 1264AL037557/1305 POLR2I polymerase (RNA) II (DNA directed) polypeptide I,14.5 kDa 212782_x_at 1265 BG335629/1306 POLR2J polymerase (RNA) II (DNAdirected) polypeptide J, 13.3 kDa 216242_x_at 1266 AW402635/1307 POLR2J2DNA directed RNA polymerase II polypeptide J-related gene 214740_at 1267BE676209/1308 POLR2J2 /// DNA directed RNA polymerase MGC13098 IIpolypeptide J-related gene /// hypothetical prote 202634_at 1268AL558030/1309 POLR2K polymerase (RNA) II (DNA directed) polypeptide K,7.0 kDa 202635_s_at 1269 NM_005034/1310 POLR2K polymerase (RNA) II (DNAdirected) polypeptide K, 7.0 kDa 202586_at 1270 AA772747/1311 POLR2Lpolymerase (RNA) II (DNA directed) polypeptide L, 7.6 kDa 211730_s_at1271 BC005903/1312 POLR2L polymerase (RNA) II (DNA directed) polypeptideL, 7.6 kDa /// polymerase (RNA) II 219459_at 1272 NM_018082/1313 POLR3Bpolymerase (RNA) III (DNA directed) polypeptide B 209382_at 1273U93867/1314 POLR3C polymerase (RNA) III (DNA directed) polypeptide C (62kD) 210573_s_at 1274 BC004424/1315 POLR3C polymerase (RNA) III (DNAdirected) polypeptide C (62 kD) 208361_s_at 1275 NM_001722/1316 POLR3Dpolymerase (RNA) III (DNA directed) polypeptide D, 44 kDa 218016_s_at1276 NM_018119/1317 POLR3E polymerase (RNA) III (DNA directed)polypeptide E (80 kD) 205218_at 1277 NM_006466/1318 POLR3F polymerase(RNA) III (DNA directed) polypeptide F, 39 kDa 206653_at 1278BF062139/1319 POLR3G Polymerase (RNA) III (DNA directed) polypeptide G(32 kD) 206654_s_at 1279 NM_006467/1320 POLR3G polymerase (RNA) III (DNAdirected) polypeptide G (32 kD) 218866_s_at 1280 AF060223/1321 POLR3Kpolymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa 203782_s_at1281 NM_005035/1322 POLRMT polymerase (RNA) mitochondrial (DNA directed)203783_x_at 1282 BF057617/1323 POLRMT polymerase (RNA) mitochondrial(DNA directed) 202466_at 1283 NM_006999/1324 POLS polymerase (DNAdirected) sigma

The measurement of RRN3, LRPPRC, POLR1D and other polymerase I mechanismrelated biomarkers could be used for diagnosis and prediction of BMS.Additionally those markers could be useful for typical RRMS patients tomonitor the efficacy of various immunomodulatory drugs for assessment ofpatients with good response to treatment.

Measurement of BMS biomarkers can be performed on the mRNA level by thequantitative reverse-transcriptase polymerase chain reaction (QRT-PCR)method and on protein level by LUMINEX technology. Possible modificationof the invention is developing biomarkers on protein level (e.g., usingELISA, Western Blot analysis and the like) in PBMC and serum.

Multiple sclerosis (MS) is a heterogeneous disease. To better diagnoseand treat MS patients the various types of disease have to bedistinguished. The teachings of the invention enable, for the firsttime, to distinguish between BMS and typical RRMS patients usingmolecular tools, which when combined with accurate clinical informationenables to dissect the biological complexity of MS.

In the current study the use of gene expression profiling enabled todiagnose benign MS using a phenotypic approach to differentiate subtypesof the disease. The identified gene expression phenotypes also enable tobetter understand the biology of benign MS and to develop therapeuticsstrategies to treat MS.

The gene expression signature generated herein of benign MS enablesrefining MS to diagnose low risk patients versus high risk patients andaccordingly suggest appropriate treatment.

The benign MS patients that represent low risk would not be treatedwhile the high risk relapsing-remitting MS patients will be treated. Inaddition, the teachings of the invention enable to monitor response totreatment and better use of current approved medications.

The teachings of the invention can be used to develop a kit or devicefor diagnosis and prediction of typical RRMS clinical outcome, improvingmedical decision support systems and individualizing patient care. Inaddition, the teachings of the invention can be used to develop newdrugs that will imitate BMS gene expression signature and will result insilencing of the active RRMS.

Example 2

Study Subject and Methods

Subjects—

31 patients (age 44.5±1.5; female to male ratio 24:7) with BMS werecharacterized by mean EDSS 1.95±0.15, disease duration 17.0±1.3 years,annual EDSS rate 0.13±0.01, annual relapse rate 0.23±0.04. 36 patients(age 40.3±1.8; female to male ratio 8:3) with RRMS were characterized bymean EDSS 3.54±0.23, disease duration 10.9±1.4 years, annual EDSS rate0.45±0.06, annual relapse rate 0.64±0.09.

RNA Isolation and Microarray Expression Profiling—

Peripheral blood mononuclear cells (PBMC) were separated onficoll-hypaque gradient. Total RNA was isolated using the TRIzol Reagent(Invitrogen, Carlsbad, Calif.), and cDNA was synthesized, labeled andhybridized to HG-U133A-2 array (Affymetrix, Inc, Santa Clara, Calif.)containing 22,215 gene-transcripts, washed and scanned (Hewlett Packard,GeneArray-TM scanner G2500A) according to manufacturer's protocolAffymetrix (Inc, Santa Clara, Calif.).

Data Analysis—

Data analysis was performed using the Partek Genomics Solution software[World Wide Web (dot) partek (dot) com]. Expression values were computedfrom raw CEL (cells) files by applying the Robust Multi-Chip Average(RMA) background correction algorithm. The RMA correction included: 1)values background correction; 2) quantile normalization; 3) log 2transformation; 4) median polish summarization. The gene transcriptswere filtered using Affymetrix MASS Present/Absent Detection.Thereafter, 9987 transcript that were detected as Present in 100%microarrays were used for analysis. In order to avoid the noise causedby variable set effects each set was normalized to pre-saveddistribution pattern of a well balanced set used as a referencedistribution. To reduce batch effect ANOVA multiple model analysis wasapplied. Source of variation was analyzed; nuisance batches effects suchas working batch, patient age, gender and treatment were eliminated.Most informative genes (MIGs) were defined as genes that passed FallsDiscavery Rate (FDR) correction with p<0.05 by ANOVA linear contrastsmodel. Thereafter, predictive algorithm based on two level crossvalidation method, Super Vector Machine (SVM) and K-Nearest Neighboralgorithms were applied to calculate MIGs classification rates. Onlygenes which were included in classifiers (from 1 to 10 genes) with morethan 70% correct classification rates were analyzed.

Experimental Results

Identification of Classification Rates of Genes Involved in the RNAPolymerase I Pathway Between Typical RRMS and BMS Disease Course—

Tables 4A-C presents the corrected classification rates for allcombinations of RRN3, LRPPRC and POLR1D genes of the RNA polymerase Ipathway for the entire BMS and typical RRMS group (Table 4A), for theBMS group (Table 4B) and for the typical RRMS group (Table 4C). The bestpredictive performance for each classifier is presented.

TABLE 4A Classifiers Aver. % Correct St. Err (%) RRN3 63.6 11.2 LRPPRC73.3 9.5 POLR1D 72.7 9.5 RRN3, POLR1D 72.7 9.5 RRN3, LRPPRC 63.6 10.2POLR1D, LRPPRC 81.8 8.2 RRN3, LRPPRC, POLR1D 77.2 8.9 Average % correct= Average percent of correct classification between BMS and typical RRMSpatients using specific classifier; St. Err. = standard error;

TABLE 4B Classifiers BMS % corr RRN3 67 LRPPRC 80 POLR1D 60 RRN3, POLR1D60 RRN3, LRPPRC 30 POLR1D, LRPPRC 80 RRN3, LRPPRC, POLR1D 70 BMS % Corr.= Average percent of correct classification for BMS patients usingspecific classifier;

TABLE 4C Classifiers Typical RRMS % corr RRN3 60 LRPPRC 67 POLR1D 80RRN3, POLR1D 83 RRN3, LRPPRC 90 POLR1D, LRPPRC 83 RRN3, LRPPRC, POLR1D83 RRMS % Corr. - Average percent of correct classification for typicalRRMS patients using specific classifier.

The results presented in Table 4B demonstrate that for classification ofBMS, each of the genes of the RNA polymerase I pathway, i.e., RRN3,LRPPRC and POLR1D exhibits a correct classification rate of 67%, 80% and60%, respectively. The results presented in Table 4C demonstrate thatfor classification of typical RRMS, each of RRN3, LRPPRC and POLR1Dexhibits a correct classification rate of 60%, 67% and 80%,respectively. In addition, an increased rate of correct classificationof typical RRMS, which is a more complex and heterogenous condition, canbe achieved using a combination of 2 or 3 genes of the RNA polymerase Ipathway. For example, a correct classification rate of 83% is obtainedusing the combination of RRN3 and POLR1D; a correct classification rateof 83% is obtained using the combination of POLR1D and LRPPRC; and acorrect classification rate of 90% is obtained using the combination ofRRN3 and LRPPRC (Table 4C, above).

The classification for the combination of RRN3 and LRPPRC resulted inoutstanding classification rate of 90% of typical RRMS (TMS) (Table 4C),while showing a low 30% classification for these 2 genes for BMS (Table4B), further supporting the differentiations between the two diseasepatterns.

To conclude, correct classification for both groups would be achievedusing more than one combination of genes of the RNA polymerase Ipathway, for example LRPPRC alone or with POLR1D reached 80%classification rate for BMS and RRN3 and LRPPRC correctly classify 90%of TMS patients.

Identification of Biomarkers for Differentiation of Patients with BMS orTypical RRMS Course of Disease—

BMS patients differentiated from typical RRMS by 177 MIGs (Table 5). The17 genes with higher classification performance (Table 6) wereidentified from MIGs by applying predictive algorithms.

TABLE 5 MIGs discriminating between BMS and typical RRMS patientsp-value Log Fold BMS Change Affymetrix vs (BMS vs ProbSet SEQRepresentative SEQ ID typical typical Gene ID NO ID: Public ID NO: RRMSRRMS) Symbol Gene description 216902_s_at 62 AF001549 468 2.12E−08 −2.01RRN3 RRN3 RNA polymerase I transcription factor homolog (yeast)210502_s_at 1410 AF042386 1534 2.30E−08 −1.28 PPIE peptidylprolylisomerase E (cyclophilin E) 211615_s_at 1418 M92439 1512 2.44E−08 −1.20LRPPRC leucine-rich PPR-motif containing /// leucine- rich PPR-motifcontaining 37950_at 1500 X74496 1526 1.05E−06 1.19 PREP prolylendopeptidase 218258_at 173 NM_015972 984 1.92E−06 −1.18 POLR1Dpolymerase (RNA) I polypeptide D, 16 kDa 214439_x_at 1453 AF043899 15352.24E−06 −1.62 BIN1 bridging integrator 1 214450_at 1454 NM_001335 16293.82E−06 −1.45 CTSW cathepsin W (lymphopain) /// cathepsin W(lymphopain) 214470_at 1455 NM_002258 1615 3.83E−06 −1.77 KLRB1 killercell lectin-like receptor subfamily B, member 1 /// killer celllectin-li 205789_at 1373 NM_001766 1627 4.32E−06 1.62 CD1D CD1D antigen,d polypeptide /// CD1D antigen, d polypeptide 206584_at 1378 NM_0153641650 5.84E−06 1.59 LY96 lymphocyte antigen 96 212252_at 1425 AA1811791660 6.14E−06 1.62 CAMKK2 calcium/calmodulin- dependent protein kinasekinase 2, beta 212748_at 1431 AB037859 1583 7.92E−06 1.18 MKL1megakaryoblastic leukemia (translocation) 1 211654_x_at 1419 M17565 15199.99E−06 2.75 HLA- major DQB1 histocompatibility complex, class II, DQbeta 1 /// major histocompatibili 204860_s_at 1370 AI817801 16731.21E−05 1.62 BIRC1 baculoviral IAP repeat- containing 1 211971_s_at 204AI653608 606 1.62E−05 −1.14 LRPPRC leucine-rich PPR-motif containing202832_at 1347 NM_014635 1601 2.21E−05 −1.33 GCC2 GRIP and coiled-coildomain containing 2 40446_at 1502 AL021366 1537 2.62E−05 −1.39 PHF1 PHDfinger protein 1 210136_at 1404 AW070431 1676 2.71E−05 −1.76 MBP Myelinbasic protein 202441_at 1342 AL568449 1691 3.92E−05 1.37 C10orf69chromosome 10 open reading frame 69 213241_at 1442 AF035307 15324.12E−05 1.55 PLXNC1 Plexin C1 212978_at 1435 AU146004 1686 4.13E−051.56 TA- T-cell activation LRRP leucine repeat-rich protein 220005_at1490 NM_023914 1591 4.55E−05 2.43 P2RY13 purinergic receptor P2Y,G-protein coupled, 13 /// purinergic receptor P2Y, G-pr 218304_s_at 1473NM_022776 1645 4.89E−05 1.58 OSBPL11 oxysterol binding protein-like 11218932_at 1480 NM_017953 1652 5.00E−05 −1.27 FLJ20729 hypotheticalprotein FLJ20729 213106_at 1440 AI769688 1670 5.57E−05 −1.51 ATP8A1ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1219892_at 1489 NM_023003 1648 5.63E−05 1.86 TM6SF1 transmembrane 6superfamily member 1 219666_at 1486 NM_022349 1585 6.07E−05 1.81 MS4A6Amembrane spanning 4- domains, subfamily A, member 6A 206120_at 1376NM_001772 1631 6.26E−05 1.58 CD33 CD33 antigen (gp67) 209970_x_at 1403M87507 1523 6.51E−05 1.33 CASP1 caspase 1, apoptosis- related cysteineprotease (interleukin 1, beta, convertase) 200980_s_at 1330 NM_0002841654 8.59E−05 −1.27 PDHA1 pyruvate dehydrogenase (lipoamide) alpha 1200610_s_at 1326 NM_005381 1613 8.97E−05 −1.17 NCL nucleolin 213418_at1445 NM_002155 1609 8.99E−05 2.73 HSPA6 heat shock 70 kDa protein 6(HSP70B′) 212421_at 1429 AB023147 1545 9.22E−05 1.66 C22orf9 chromosome22 open reading frame 9 210201_x_at 1407 AF001383 1531 9.59E−05 −1.59BIN1 bridging integrator 1 207000_s_at 1381 NM_005605 1600 9.72E−05−1.32 PPP3CC protein phosphatase 3 (formerly 2B), catalytic subunit,gamma isoform (calcineur 203139_at 1352 NM_004938 1623 0.000102879 1.78DAPK1 death-associated protein kinase 1 211368_s_at 1416 U13700 15270.000107311 1.36 CASP1 caspase 1, apoptosis- related cysteine protease(interleukin 1, beta, convertase) 212820_at 1433 AB020663 15820.000108529 1.70 RC3 rabconnectin-3 216945_x_at 15 U79240 4210.000111457 −1.86 PASK PAS domain containing serine/threonine kinase209337_at 1395 AF063020 1540 0.000112781 −1.35 PSIP1 PC4 and SFRS1interacting protein 1 201756_at 1337 NM_002946 1599 0.000114388 −1.41RPA2 replication protein A2, 32 kDa 221565_s_at 1493 BC000039 16020.00011473 1.50 FAM26B family with sequence similarity 26, member B117_at 1325 X51757cds #N/A 0.000116998 2.01 HSPA6 heat shock 70 kDaprotein 6 (HSP70B′) 43544_at 1503 AA314406 1661 0.000118986 −1.65 THRAP5thyroid hormone receptor associated protein 5 219132_at 1483 NM_0212551621 0.000121966 1.36 PELI2 pellino homolog 2 (Drosophila) 57715_at 1507W72694 1657 0.000123909 1.35 FAM26B family with sequence similarity 26,member B 220066_at 1491 NM_022162 1569 0.000125076 1.53 CARD15 caspaserecruitment domain family, member 15 212414_s_at 1428 D50918 15280.000139145 −1.53 SEPT6 septin 6 213902_at 1448 AI379338 16660.000139994 1.32 ASAH1 N-acylsphingosine amidohydrolase (acidceramidase) 1 212998_x_at 1436 AI583173 1667 0.000143667 2.26 HLA- majorDQB1 histocompatibility complex, class II, DQ beta 1 /// majorhistocompatibili 202931_x_at 1350 NM_004305 1584 0.000148834 −1.55 BIN1bridging integrator 1 204112_s_at 1361 NM_006895 1619 0.00014954 1.81HNMT histamine N- methyltransferase 205467_at 297 NM_001230 8500.000150498 1.44 CASP10 caspase 10, apoptosis related cysteine protease209199_s_at 1394 N22468 1656 0.000157534 1.51 MEF2C MADS boxtranscription enhancer factor 2, polypeptide C (myocyte enhancer factor211676_s_at 1421 AF056979 1578 0.000157969 1.40 IFNGR1 interferon gammareceptor 1 /// interferon gamma receptor 1 203492_x_at 1355 AA9182241664 0.000163582 −1.22 KIAA0092 translokin 211776_s_at 1423 BC0061411577 0.000164075 3.18 EPB41L3 erythrocyte membrane protein band 4.1-like3 /// erythrocyte membrane protein ba 56919_at 1505 AI806628 16720.000173847 1.32 KIAA1449 WD repeat endosomal protein 202521_at 1344NM_006565 1616 0.0001784 −1.14 CTCF CCCTC-binding factor (zinc fingerprotein) 211727_s_at 1422 BC005895 1576 0.000179886 −1.49 COX11 COX11homolog, cytochrome c oxidase assembly protein (yeast) /// COX11homolog, 204222_s_at 1363 NM_006851 1628 0.00018487 1.54 GLIPR1 GLIpathogenesis- related 1 (glioma) 204839_at 1369 NM_015918 16030.000185062 −1.21 POP5 processing of precursor 5, ribonuclease P/MRPsubunit (S. cerevisiae) 39729_at 1501 L19185 1524 0.000185886 −1.62PRDX2 peroxiredoxin 2 221078_s_at 1492 NM_018084 1646 0.000188529 1.49KIAA1212 KIAA1212 35156_at 1499 AL050297 1548 0.000196739 −1.24LOC203069 Hypothetical protein LOC203069 219630_at 1485 NM_005764 16060.000198793 1.94 MAP17 membrane-associated protein 17 202662_s_at 1345NM_002223 1625 0.00020557 1.34 ITPR2 inositol 1,4,5- triphosphatereceptor, type 2 210212_x_at 1409 BC002600 1571 0.000219441 −1.27 MTCP1mature T-cell proliferation 1 217925_s_at 1471 NM_022758 16100.000224904 −1.21 C6orf106 chromosome 6 open reading frame 106 218739_at1477 NM_016006 1643 0.000228499 1.75 ABHD5 abhydrolase domain containing5 56197_at 1504 AI783924 1671 0.000231008 −1.24 PLSCR3 phospholipidscramblase 3 208653_s_at 1388 AF263279 1561 0.00023174 1.46 CD164 CD164antigen, sialomucin 213292_s_at 1444 AA908770 1663 0.00023191 1.54 SNX13sorting nexin 13 201194_at 1331 NM_003009 1608 0.000240228 −1.36 SEPW1selenoprotein W, 1 201619_at 1336 NM_006793 1596 0.000250445 1.27 PRDX3peroxiredoxin 3 203569_s_at 1356 NM_003611 1640 0.000272476 −1.45 OFD1oral-facial-digital syndrome 1 213979_s_at 1450 BF984434 1689 0.00027541−3.22 — — 203814_s_at 1359 NM_000904 1635 0.000281273 1.67 NQO2 NAD(P)Hdehydrogenase, quinone 2 215118_s_at 1462 AW519168 1680 0.000302493−2.77 MGC27165 Hypothetical protein MGC27165 203624_at 1357 NM_0050881607 0.000330513 −1.38 DXYS155E DNA segment on chromosome X and Y(unique) 155 expressed sequence 206999_at 1380 NM_001559 15880.000344019 2.07 IL12RB2 interleukin 12 receptor, beta 2 205842_s_at1374 AF001362 1538 0.000351718 1.85 JAK2 Janus kinase 2 (a proteintyrosine kinase) 210166_at 1405 AF051151 1536 0.000353968 1.63 TLR5toll-like receptor 5 219714_s_at 1487 NM_018398 1612 0.000364622 2.39CACNA2D3 calcium channel, voltage-dependent, alpha 2/delta 3 subunit212311_at 1426 AA522514 1662 0.000370292 −1.36 KIAA0746 KIAA0746 protein213830_at 1447 AW007751 1675 0.000370999 −1.69 TRD @ T-cell receptordelta chain HE/801 /// T cell receptor delta locus 213005_s_at 1438D79994 1614 0.000376513 2.26 ANKRD15 ankyrin repeat domain 15 202944_at1351 NM_000262 1639 0.000376931 1.68 NAGA N- acetylgalactosaminidase,alpha- 206011_at 1375 AI719655 1668 0.000379898 1.49 CASP1 caspase 1,apoptosis- related cysteine protease (interleukin 1, beta, convertase)204332_s_at 1365 M64073 1516 0.000382893 −1.22 AGAaspartylglucosaminidase 215592_at 1463 AU147620 1687 0.000385413 −1.91 —Transcribed locus, weakly similar to XP_375099.1 hypothetical proteinLOC283585 201798_s_at 378 NM_013451 777 0.000387903 2.24 FER1L3fer-1-like 3, myoferlin (C. elegans) 212069_s_at 1424 AK026025 15660.000388281 −1.17 KIAA0515 KIAA0515 206255_at 1377 NM_001715 15970.000395152 −1.72 BLK B lymphoid tyrosine kinase 221932_s_at 1497AA133341 1658 0.000396589 −1.42 C14orf87 chromosome 14 open readingframe 87 203246_s_at 1353 NM_006545 1611 0.000402598 −1.33 TUSC4 tumorsuppressor candidate 4 213534_s_at 19 D50925 425 0.000408073 −1.73 PASKPAS domain containing serine/threonine kinase 219045_at 1481 NM_0190341604 0.000412198 −1.33 RHOF ras homolog gene family, member F (infilopodia) 202347_s_at 1340 AB022435 1550 0.000414497 −1.16 HIP2huntingtin interacting protein 2 212636_at 1430 AL031781 15430.000420707 1.61 QKI quaking homolog, KH domain RNA binding (mouse)202392_s_at 1341 NM_014338 1598 0.000423758 1.26 PISD phosphatidylserinedecarboxylase 216950_s_at 1467 X14355 1509 0.000437652 2.62 FCGR1A Fcfragment of IgG, high affinity Ia, receptor for (CD64) 214511_x_at 1457L03419 1515 0.000447516 2.83 LOC440607 Fc-gamma receptor I /// B2 /// Fcfragment of FCGR1A IgG, high affinity Ia, receptor for (C 219316_s_at1484 NM_017791 1641 0.000472922 1.68 C14orf58 chromosome 14 open readingframe 58 220122_at 398 NM_024717 797 0.000473634 3.36 MCTP1 multipleC2-domains with two transmembrane regions 1 64883_at 1508 AI744083 16690.000478581 1.51 MOSPD2 motile sperm domain containing 2 203279_at 1354NM_014674 1644 0.000479669 −1.24 EDEM1 ER degradation enhancer,mannosidase alpha-like 1 208891_at 1390 BC003143 1573 0.000483009 1.98DUSP6 dual specificity phosphatase 6 205715_at 1372 NM_004334 16360.000490107 1.60 BST1 bone marrow stromal cell antigen 1 214085_x_at1451 AI912583 1674 0.000510466 1.67 HRB2 HIV-1 rev binding protein 2215000_s_at 1461 AL117593 1553 0.000515959 1.24 FEZ2 fasciculation andelongation protein zeta 2 (zygin II) 202194_at 1339 AL117354 15560.000523169 1.36 CGI- CGI-100 protein 100 210202_s_at 1408 U87558 15300.000532952 −1.46 BIN1 bridging integrator 1 218181_s_at 1472 NM_0177921560 0.000547382 1.13 MAP4K4 mitogen-activated protein kinase kinasekinase kinase 4 204023_at 1360 NM_002916 1595 0.000553752 −1.48 RFC4replication factor C (activator 1) 4, 37 kDa 207872_s_at 1384 NM_0068631551 0.000561178 1.58 LILRA1 leukocyte immunoglobulin-like receptor,subfamily A (with TM domain), member 1 202878_s_at 1349 NM_012072 16220.000583921 1.42 C1QR1 complement component 1, q subcomponent, receptor1 201285_at 1333 NM_013446 1649 0.000593976 −1.21 MKRN1 makorin, ringfinger protein, 1 /// makorin, ring finger protein, 1 211612_s_at 1417U62858 1529 0.000613797 1.80 IL13RA1 interleukin 13 receptor, alpha 1/// interleukin 13 receptor, alpha 1 219117_s_at 1482 NM_016594 16470.000616534 −1.61 FKBP11 FK506 binding protein 11, 19 kDa 215761_at 1464AK000156 1557 0.000618215 2.26 RC3 rabconnectin-3 200800_s_at 1328NM_005345 1642 0.000625103 1.65 HSPA1A heat shock 70 kDa /// protein 1A/// heat HSPA1B shock 70 kDa protein 1B 202816_s_at 1346 AW292882 16790.000641212 1.44 SS18 synovial sarcoma translocation, chromosome 18209440_at 1397 BC001605 1572 0.000646328 −1.25 PRPS1 phosphoribosylpyrophosphate synthetase 1 204221_x_at 1362 U16307 1587 0.000654803 1.51HRB2 HIV-1 rev binding protein 2 57082_at 1506 AA169780 1659 0.000658787−1.41 ARH LDL receptor adaptor protein 201887_at 1338 NM_001560 15890.000679598 1.52 IL13RA1 interleukin 13 receptor, alpha 1 215933_s_at1465 Z21533 1510 0.000692626 1.47 HHEX hematopoietically expressedhomeobox 208774_at 1389 AV700224 1685 0.000699738 1.20 CSNK1D Caseinkinase 1, delta 201478_s_at 1334 U59151 1533 0.000707429 −1.18 DKC1dyskeratosis congenita 1, dyskerin 208918_s_at 1391 AI334128 16650.000708781 1.38 FLJ13052 NAD kinase 208158_s_at 1386 NM_018030 15810.000726407 1.37 OSBPL1A oxysterol binding protein-like 1A /// oxysterolbinding protein-like 1A 202838_at 1348 NM_000147 1651 0.00073801 1.43FUCA1 fucosidase, alpha-L-1, tissue 205039_s_at 1371 NM_006060 16330.000754874 2.05 ZNFN1A1 zinc finger protein, subfamily 1A, 1 (Ikaros)204834_at 1368 NM_006682 1626 0.000760238 1.74 FGL2 fibrinogen-like 2200701_at 1327 NM_006432 1592 0.000763959 1.41 NPC2 Niemann-Pickdisease, type C2 204254_s_at 1364 NM_000376 1617 0.00077458 1.64 VDRvitamin D (1,25- dihydroxyvitamin D3) receptor 217922_at 1470 AL1579021562 0.000779841 −1.34 MAN1A2 Mannosidase, alpha, class 1A, member 2218888_s_at 1479 NM_018092 1586 0.000801694 1.39 NETO2 neuropilin (NRP)and tolloid (TLL)-like 2 210947_s_at 1414 J04810 1514 0.000810544 1.30MSH3 mutS homolog 3 (E. coli) 208923_at 1392 BC005097 1575 0.0008161091.41 CYFIP1 cytoplasmic FMR1 interacting protein 1 209429_x_at 1396AF112207 1555 0.000818155 −1.22 — — 204566_at 1366 NM_003620 15930.000823091 1.67 PPM1D protein phosphatase 1D magnesium-dependent, deltaisoform 218854_at 1478 NM_013352 1630 0.000823847 1.47 SART2 squamouscell carcinoma antigen recognized by T cells 2 213198_at 1441 AL1176431554 0.000836 1.33 ACVR1B activin A receptor, type IB 218642_s_at 1476NM_024300 1618 0.000849263 −1.21 CHCHD7 coiled-coil-helix-coiled-coil-helix domain containing 7 203645_s_at 1358 NM_004244 16320.000851877 1.60 CD163 CD163 antigen 208117_s_at 1385 NM_031206 16530.000852389 −1.32 FLJ12525 hypothetical protein FLJ12525 ///hypothetical protein FLJ12525 218519_at 1474 NM_017945 1594 0.0008540141.30 SLC35A5 solute carrier family 35, member A5 217764_s_at 1469AF183421 1563 0.000871159 1.30 RAB31 RAB31, member RAS oncogene family214765_s_at 1459 AK024677 1564 0.000919505 1.50 ASAHL N-acylsphingosineamidohydrolase (acid ceramidase)-like 212799_at 1432 BE217875 16820.00093697 1.31 — Clone 23570 mRNA sequence 204744_s_at 1367 NM_0134171624 0.000961709 −1.24 IARS isoleucine-tRNA synthetase 218526_s_at 1475NM_014185 1559 0.000964651 −1.22 RANGNRF RAN guanine nucleotide releasefactor 211139_s_at 1415 AF045452 1539 0.000972219 1.40 NAB1 NGFI-Abinding protein 1 (EGR1 binding protein 1) 213958_at 1449 AW134823 16770.000977101 −1.39 CD6 CD6 antigen /// CD6 antigen 221695_s_at 1494AF239798 1558 0.000979214 1.37 MAP3K2 mitogen-activated protein kinasekinase kinase 2 /// mitogen- activated protein k 210176_at 1406 AL0502621549 0.000989413 1.62 TLR1 toll-like receptor 1 212314_at 1427 AB0182891542 0.00099 −1.34 KIAA0746 KIAA0746 protein 209882_at 1402 AF0844621544 0.000992617 1.42 RIT1 Ras-like without CAAX 1 214500_at 1456AF044286 1541 0.00102256 1.51 H2AFY H2A histone family, member Y213088_s_at 1439 BE551340 1684 0.00104481 −1.17 DNAJC9 DnaJ (Hsp40)homolog, subfamily C, member 9 200821_at 1329 NM_013995 1638 0.001045511.22 LAMP2 lysosomal-associated membrane protein 2 210732_s_at 1411AF342816 1574 0.00106818 1.84 LGALS8 lectin, galactoside- binding,soluble, 8 (galectin 8) 201224_s_at 1332 AU147713 1688 0.00107129 −1.23SRRM1 serine/arginine repetitive matrix 1 202444_s_at 1343 NM_0064591634 0.00107236 1.72 C10orf69 chromosome 10 open reading frame 69206707_x_at 1379 NM_015864 1580 0.00107472 −1.24 C6orf32 chromosome 6open reading frame 32 221839_s_at 1496 AK026088 1567 0.00107916 −1.34UBAP2 ubiquitin associated protein 2 213279_at 1443 AL050217 15470.00108194 1.21 DHRS1 dehydrogenase/reductase (SDR family) member 1214974_x_at 1460 AK026546 1568 0.00109223 2.67 CXCL5 chemokine (C—X—Cmotif) ligand 5 209583_s_at 1399 AF063591 1570 0.00109644 1.65 CD200CD200 antigen 209870_s_at 1401 AW571582 1681 0.00112322 −1.39 APBA2amyloid beta (A4) precursor protein- binding, family A, member 2(X11-like) 201494_at 1335 NM_005040 1605 0.0011371 1.27 PRCPprolylcarboxypeptidase (angiotensinase C) 219806_s_at 1488 NM_0201791637 0.00113985 1.36 FN5 FN5 protein 208651_x_at 1387 M58664 15130.00119019 −1.38 CD24 CD24 antigen (small cell lung carcinoma cluster 4antigen) 216191_s_at 1466 X72501 1522 0.00132593 −1.84 TRDD3 T cellreceptor delta /// diversity 3 /// T cell TRD @ receptor delta locus217143_s_at 1468 X06557 1511 0.00187286 −1.83 TRDD3 T cell receptordelta /// diversity 3 /// T cell TRD @ receptor delta locus vs. =versus.

TABLE 6 Genes which when included in classifiers of no more than 10genes exhibit at least 70% correct classification rates between BMS andtypical RRMS patients Full P BMS Sequence SEQ Length SEQ Probeset SEQ IDGene value vs Derived ID Ref. ID ID NO: Symbol (min) RRMS From NO: GeneTitle Sequences NO: 222204_s_at 1498 RRN3 2.1 * 10−8 (−) AL110238 1552RNA NM_018427 1010 polymerase I transcription factor RRN3 221714_s_at1495 LOC94431 BC006441 1579 similar to RNA NM_145237 1156 polymerase Itranscription factor RRN3 211615_s_at 1418 LRPPRC 2.4 * 10−8 (−) M924391512 leucine-rich NM_133259 1065 PPR-motif containing protein211971_s_at 204 LRPPRC AI653608 606 leucine-rich NM_133259 1065 PPRmotif containing protein 218258_at 173 POLR1D 1.9 * 10−6 (−) NM_015972984 hypothetical NM_152705 1695 protein MGC9850 205789_at 1373 CD1D4.3 * 10−6 (+) NM_001766 1627 CD1D antigen, NM_001766 1627 d polypeptide212999_x_at 1437 HLA- 9.9 * 10−6 (+) AW276186 1678 major NM_002123 1699DQB1 histocompatibility complex, class II, DQ beta 1 precursor209823_x_at 1400 HLA- M17955 1518 major NM_002123 1699 DQB1histocompatibility complex, class II, DQ beta 1 precursor 209480_at 1398HLA- M16276 1521 major NM_002123 1699 DQB1 histocompatibility complex,class II, DQ beta 1 precursor 211656_x_at 1420 HLA- M32577 1520 majorNM_002123 1699 DQB1 histocompatibility complex, class II, DQ beta 1precursor 211654_x_at 1419 HLA- M17565 1519 major NM_002123 1699 DQB1histocompatibility complex, class II, DQ beta 1 precursor 210747_at 1412HLA- M24364 1525 major NM_002123 1699 DQB1 histocompatibility complex,class II, DQ beta 1 precursor 206584_at 1378 LY96 5.8 * 10−6 (+)NM_015364 1650 lymphocyte NM_015364 1650 antigen 96; // MD-2 protein207359_at 1383 CAMKK2 6.1 * 10−6 (+) NM_006549 1590 calcium/calmodulin-NM_006549 1590 dependent protein kinase kinase 2, beta isoform 1214209_s_at 1452 CAMKK2 BE504895 1683 calcium/calmodulin- NM_006549 1590dependent protein kinase kinase 2, beta isoform 1 213812_s_at 1446CAMKK2 AK024748 1565 calcium/calmodulin- NM_006549 1590 dependentprotein kinase kinase 2, beta isoform 1 210787_s_at 1413 CAMKK2 AF1405071546 calcium/calmodulin- NM_006549 1590 dependent protein kinase kinase2, beta isoform 1 212252_at 1425 CAMKK2 AA181179 1660calcium/calmodulin- NM_006549 1590 dependent protein kinase kinase 2,beta isoform 1 214643_x_at 1458 BIN1 2.2 * 10−6 (−) BG034080 1690bridging NM_004305 1693 integrator 1 // //1694 isoform 8 NM_139343210202_s_at 1408 BIN1 U87558 1530 bridging NM_004305 1693 integrator 1// //1694 isoform 8 NM_139343 // 214439_x_at 1453 BIN1 AF043899 1535bridging NM_004305 1693 integrator 1 // //1694 isoform 8 NM_139343 //202931_x_at 1350 BIN1 NM_004305 1584 bridging NM_004305 1693 integrator1 // //1694 isoform 8 NM_139343 // 210201_x_at 1407 BIN1 AF001383 1531bridging NM_004305 1693 integrator 1 // //1694 isoform 8 NM_139343 //214450_at 1454 CTSW 3.8 * 10−6 (−) NM_001335 1629 cathepsin W NM_0013351629 preproprotein 214470_at 1455 KLRB1 3.8 * 10−6 (−) NM_002258 1615killer cell lectin- NM_002258 1615 like receptor subfamily B, member 1212748_at 1431 MKL1 7.9 * 10−9 (+) AB037859 1583 megakaryoblasticNM_020831 1696 leukemia (translocation) 1 209072_at 1393 MBP 2.7 * 10−5(−) M13577 1517 myelin basic NM_002385 1620 protein 210136_at 1404 MBPAW070431 1676 myelin basic NM_002385 1620 protein 207323_s_at 1382 MBPNM_002385 1620 myelin basic NM_002385 1620 protein 212978_at 1435 TA-4.1 * 10−5 (+) AU146004 1686 T-cell activation NM_015350 1700 LRRPleucine repeat- rich protein 212976_at 1434 TA- R41498 1655 T-cellactivation NM_015350 1700 LRRP leucine repeat- rich protein 117_at 1325HSPA6 8.9 * 10−5 (+) X51757 1692 heat shock NM_002155 1609 70 kDaprotein 6 (HSP70B′) 213418_at 1445 HSPA6 NM_002155 1609 heat shockNM_002155 1609 70 kDa protein 6 (HSP70B′) 200610_s_at 1326 NCL 8.9 *10−5 (−) NM_005381 1613 nucleolin NM_005381 1613 216191_s_at 1466 TRD @3.7 * 10−4 (−) X72501 1522 T cell receptor — #N/A delta locus217143_s_at 1468 TRD @ X06557 1511 T cell receptor — #N/A delta locus213830_at 1447 TRD @ AW007751 1675 T cell receptor — #N/A delta locus213005_s_at 1438 KANK 3.7 * 10−4 (+) D79994 1614 kidney ankyrinNM_015158 1698 repeat- // //1697 containing NM_153186 protein Presentedare 38 gene transcripts which correspond for 17 human genes whichclassify BMS and typical RRMS patients. Genes given by the gene name anddescription, the Affymetrix probeset identification number, and arepresentative GenBank Accession numbers. The (−) sign means that thepolynucleotide is downregulated (decreased in level) in BMS as comparedto typical RRMS subjects; and the (+) sign means that the polynucleotideis upregulated (increased in level) in BMS as compared to RRMS subjects.

Examples of classifiers are presented as following:

NCL, MKL1, CTSW, KLRB1 and LRPPRC which results in correctclassification rate of 79% of BMS and typical RRMS; and NCL, MKL1, CTSW,KLRB1, POLR1D, CD1D, and CAMKK2 which results in correct classificationrate of 77% of BMS and typical RRMS.

Example 3 Testing the Effect of an Anti MS Drug in Experimental AllergicEncephalomyelitis (EAE)—Animal MS Model

Animal Model for Multiple Sclerosis—

EAE is induced in female Lewis rats (N=15; 6-8 weeks old, body weight180-200 g) by hind footpad subcutaneous inoculation with emulsion of 25mg guinea-pig MBP (myelin basic protein) in CFA containing 40 mg ofMycobacterium tuberculosis (Difco, Detroit, Mich.) in 0.1 ml oil.Control rats (N=15) are injected with the same emulsion where salinesolution replaces MBP. The EAE is scored as follows: 0—No obviouschanges in motor function on of the rats in comparison to non-immunizedrats; 1—Limp tail; 2—Limp tail and weakness of hind legs; 3—Limp tailand complete paralysis of hind legs, or limp tail with paralysis of onefront and one hind leg. Or all of: walking only along the edges of thecage, pushing against the cage wall, pushing against the cage wall,spinning when picked up by the tail; 4—Limp tail, complete hind leg andpartial front leg paralysis; 5—Complete hind and complete front legparalysis, no movement around the cage, or mouse is spontaneouslyrolling in the cage, mouse is found dead due to paralysis.

Treatment with an Anti MS Drug or with an Agent which Downregulates atLeast One Gene of the RNA Polymerase Pathway—

A therapeutically effective amount of a drug or an agent whichdownregulates the expression level of a gene involved in the RNApolymerase I pathway (e.g., TPT) is administered to the animal on theday of EAE induction and blood samples are drawn before and aftertreatment, at predetermined time points which include baseline=Time 0,Day 12—peak disease, Day 17 and day 21.

Testing the Level of Expression of Genes Involved in the RNA PolymeraseI Pathway—

Blood samples, obtained from the control and treated animals, are testedusing Q-RT-PCR for bio-markers of benign multiple sclerosis (e.g., RRN₃,POLR₁D and LRPPRC). Control animals are compared to animals on the peakof EAE disease and to animals treated by the anti MS drug (e.g., TPT).

Example 4 In Vitro Testing Efficacy of a Drug In Vitro Using Cells of aMultiple Sclerosis Subject

Peripheral blood samples are obtained from female subjects with typicalRRMS disease course. All patients are free of immunomodulatory orcorticosteroid treatments at least 30 days before blood withdrawal. PBMCare extracted from peripheral blood, separated by Ficoll-Hypaquegradient. 15 ml of peripheral blood from patients is diluted 1:1 withPhosphate Buffered Saline (PBS) (without Ca²⁺/Mg²⁺). Blood samples areunderlied with 10 ml of Ficoll-Lymphoprep (Axis Chield, Norway) andspinned (Eppendorf centrifuge, Germany) at 2300 RPM for 30 minutes.PBMCs are collected, washed with PBS and counted and incubated at 37° C.in a humidified CO₂ incubator with or without anti MS drugs. Afterincubation, total RNA is extracted using both Trizol (Invitrogen, USA)and Phase-Lock-Gel columns (Eppendorf, Germany) including a DNasedigestion step. RNA integrity is assessed by RNA Experion automatedelectrophoresis system.

Treatment with an Anti MS Drug or with an Agent which Downregulates atLeast One Gene of the RNA Polymerase Pathway—

A therapeutically effective amount of a drug or an agent whichdownregulates the expression level of a gene involved in the RNApolymerase I pathway (e.g., TPT) is incubated during 3 hours with thePBMC (of the subject having typical RRMS) and compared with PBMC (of thesubject having typical RRMS) incubated during 3 hours without drug orwith placebo excluding therapeutic component.

Testing the Level of Expression of Genes Involved in the RNA PolymeraseI Pathway—

Total RNA samples, obtained from PBMC of a subject having typical RRMStrayed in-vitro with anti-RNA polymerase I agents (e.g. TPT), are testedusing Q-RT-PCR for bio-markers of benign multiple sclerosis (e.g., RRN₃,POLR₁D and LRPPRC). The results compared with PBMC from same patientsincubated without drag or with placebo.

Although the invention has been described in conjunction with specificembodiments thereof, it is evident that many alternatives, modificationsand variations will be apparent to those skilled in the art.Accordingly, it is intended to embrace all such alternatives,modifications and variations that fall within the spirit and broad scopeof the appended claims.

All publications, patents and patent applications mentioned in thisspecification are herein incorporated in their entirety by referenceinto the specification, to the same extent as if each individualpublication, patent or patent application was specifically andindividually indicated to be incorporated herein by reference. Inaddition, citation or identification of any reference in thisapplication shall not be construed as an admission that such referenceis available as prior art to the present invention. To the extent thatsection headings are used, they should not be construed as necessarilylimiting.

REFERENCES Additional References are Cited in Text

-   1. Hirschler-Laszkiewicz I, Cavanaugh A H, Mirza A et al. Rrn3    becomes inactivated in the process of ribosomal DNA transcription. J    Biol Chem. 2003; 278:18953-18959;-   2. Miller G, Panov K I, Friedrich J K et al. hRRN3 is essential in    the SL1-mediated recruitment of RNA Polymerase I to rRNA gene    promoters. Embo J. 2001; 20:1373-1382;-   3. Achiron A, Gurevich M, Snir Y et al Zinc-ion binding and cytokine    activity regulation pathways predicts outcome in relapsing-remitting    multiple sclerosis. Clin Exp Immunol. 2007; 149:235-242;-   4. Mootha V K, Lepage P, Miller K et al. Identification of a gene    causing human cytochrome c oxidase deficiency by integrative    genomics. Proc Natl Acad Sci USA. 2003; 100:605-610;-   5. Bouwmeester T, Bauch A, Ruffner H et al. A physical and    functional map of the human TNF-alpha/NF-kappa B signal transduction    pathway. Nat Cell Biol. 2004; 6:97-105;-   6. Leuenroth S J, Crews C M. Triptolide-induced transcriptional    arrest is associated with changes in nuclear substructure. Cancer    Res. 2008; 68:5257-5266;-   7. Liu Y, Chen Y, Lamb J R, Tam P K. Triptolide, a component of    Chinese herbal medicine, modulates the functional phenotype of    dendritic cells. Transplantation. 2007; 84:1517-1526;-   8. Wang Y, Mei Y, Feng D, Xu L. Triptolide modulates T-cell    inflammatory responses and ameliorates experimental autoimmune    encephalomyelitis. J Neurosci Res. 2008; 86:2441-2449;-   9. Pittock S J, Rodriguez M. Benign multiple sclerosis: a distinct    clinical entity with therapeutic implications. Curr Top Microbiol    Immunol. 2008; 318:1-17;-   10. L Costelloe, A Thompson, C Walsh, N Tubridy, and M Hutchinson    Long-term clinical relevance of criteria for designating multiple    sclerosis as benign after 10 years of disease J. Neurol. Neurosurg.    Psychiatry, November 2008; 79: 1245-1248.

What is claimed is:
 1. A composition comprising a probeset forclassifying a disease course in a subject diagnosed with multiplesclerosis comprising a plurality of oligonucleotides and no more than 50oligonucleotides, wherein said plurality of oligonucleotides compriseoligonucleotides that specifically recognize RRN3, POLR1D and LRPPRC;and a biological sample of a subject diagnosed with multiple sclerosis.2. The composition of claim 1, wherein said biological sample comprisesa blood sample.
 3. The composition of claim 1, wherein said plurality ofoligonucleotides comprises no more than 25 oligonucleotides.
 4. Thecomposition of claim 1, wherein said classifying a disease coursecomprises distinguishing between benign multiple sclerosis (BMS) andrelapsing-remitting multiple sclerosis (RRMS).